# pair_qualities

quality: tissue-paired
description:
  In well paired samples, a tissue is seperated into several parts, which are sequenced using different technologies.


quality: sample-paired
description:
  In sample-paired samples, different tissues from a patient is selected and sequenced by different technologies.


quality: pathological-paired
description:
  In pathological-paired samples, tissues are selected from different patients but with same pathological characheristics, and are sequenced by different technologies.


quality: species-paired
description:
  species-paired samples are from the same species but without pathological associations. They are sequenced by different technologies.


# datasets

dataset_id: STDS0000236
title: A spatial transcriptome map of developing maize ear
species: Maize
tissues: Ear
technologies: Stereo-Seq;scRNA
disease: Plants
submission_date: 2023-11-02 00:00:00
last_modified: 2023-11-02 00:00:00
contributors: Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Da
contacts: ningy@mail.hzau.edu.cn
accessions: https://db.cngb.org/search/project/CNP0004249/
platforms: BGISEQ-1000
has_paired: STDS0000236
summary:
  In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of developing maize ear primordia.

overall_design:
  Maize 6mm ear were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing


dataset_id: STDS0000235
title: Spatial transcriptomics map of the embryonic mouse brain – a tool to explore neurogenesis
species: Mus musculus
tissues: Brain
development_stages: E13.5
sex: F | M
technologies: 10x Visium
disease: Brain cortex
submission_date: 2023-08-11 00:00:00
last_modified: 2023-10-13 00:00:00
contributors: Di Marco B;Vázquez-Marín J;Monyer H;Centanin L;Alfonso J
contacts: jvazmar89@gmail.com;javier.vazquez@cos.uni-heidelberg.de
accessions: https://db.cngb.org/stomics/project/STT0000051
platforms: GPL24247
pmid: 37855382
has_paired: SCDS0000001
summary:
  The developing brain has a complex and well-organized anatomical structure comprising different types of neural and non-neural cells. Stem cells, progenitors, and newborn neurons tightly interact with their neighbouring cells and tissue microenvironment, and this intricate interplay ultimately shapes the output of neurogenesis. Given the relevance of spatial cues during brain development, we acknowledge the necessity for a transcriptomics atlas within the tissue context accessible to the neurodevelopmental community. To fulfil this need, we offer an open-access spatial gene expression browser of the embryonic mouse brain at the peak of neurogenesis. Using 10x Visium technology, we generated spatially-resolved RNAseq data from E13.5 embryonic brain sections. Unsupervised clustering reliably defined specific cell type populations of diverse lineages and maturational states. Differential expression analysis revealed unique transcriptional signatures across specific embryonic brain areas, uncovering novel features inherent to particular anatomical domains. Furthermore, we integrated single-cell RNAseq data from E13.5 mouse brains into our Spatial Transcriptomics data, adding tissue context to single-cell resolution. In summary, we provide a valuable tool that enables the exploration and discovery of unforeseen molecular players involved in neurogenesis, particularly in the crosstalk between different cell types.

overall_design:
  Four sections from four different WT mouse embryonic heads (stage E13.5) were extracted for spatial transcriptomics using the 10x Genomics Visium platform in order to identify areas of the embryonic brain with different cell lineages and maturation states at the peak of neurogenesis.

citation:
  Di Marco, Barbara et al. “Spatial transcriptomics map of the embryonic mouse brain - a tool to explore neurogenesis.” Biology open vol. 12,10 (2023): bio060151. doi:10.1242/bio.060151


dataset_id: STDS0000234
title: SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics
species: Mus musculus
tissues: Brain
development_stages: Puberscent
sex: Male
technologies: Stereo-Seq
disease: Normal atlas
submission_date: 2023-06-10 00:00:00
last_modified: 2023-09-07 00:00:00
contacts: gongchun@mgi-tech.com
platforms: DNBSEQ-T10
has_paired: SCDS0000016
summary:
  The basic analysis steps of spatial transcriptomics involves obtaining gene expression information from both space and cells. This process requires a set of tools to be completed, and existing tools face performance issues when dealing with large data sets. These issues include computationally intensive spatial localization, RNA genome alignment, and excessive memory usage in large chip scenarios. These problems affect the applicability and efficiency of the process. To address these issues, a high-performance and accurate spatial transcriptomics data analysis workflow called Stereo-Seq Analysis Workflow (SAW) has been developed for the Stereo-Seq technology developed by BGI. This workflow includes mRNA spatial position reconstruction, genome alignment, gene expression matrix generation and clustering, and generate results files in a universal format for subsequent personalized analysis. The excutation time for the entire analysis process is ~148 minutes on 1G reads 1*1 cm chip test data, 1.8 times faster than unoptimized workflow.

contributors:
  Chun Gong;Shengkang Li;Leying Wang;Fuxiang Zhao;Shuangsang Fang;Dong Yuan;Zijian Zhao;Qiqi He;Mei Li;Weiqing Liu;Zhaoxun Li;Hongqing Xie;Sha Liao;Ao Chen;Yong Zhang;Yuxiang Li;Xun Xu


dataset_id: STDS0000212
species: Homo sapiens
tissues: Skin
organ_parts: Atopic dermatitis lesional skin;Atopic dermatitis non-lesional skin;Skin
technologies: 10x Visium
disease: Atopic dermatitis
submission_date: 2022-02-18 00:00:00
last_modified: 2023-08-11 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197023
platforms: Illumina NovaSeq 6000
pmid: 37312623
has_paired: SCDS0000002
title:
  Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis [ST]

summary:
  Atopic dermatitis (AD) is the most common chronic inflammatory skin disease with complex pathogenesis. Using spatial and single-cell transcriptomics of whole skin biopsy and suction blister material, we investigated the cellular and molecular features of the leukocyte-infiltrated area in AD. We identified unique clusters of fibroblasts, dendritic cells, macrophages, and T cells in the lesional AD skin and molecular interactions between these cells. The leukocyte-infiltrated areas in lesional AD skin showed upregulation of COL6A5, COL4A1, TNC, IL32, CCL19 in COL18A1-expressing fibroblasts. Additionally, M2 macrophages expressed CCL13 and CCL18 in the same localization. Ligand–receptor interaction analysis of the spatial transcriptome identified a neighboring infiltration and interaction between activated COL18A1-expressing fibroblasts, activated CCL13- and CCL18-expressing M2 macrophages, CCR7- and LAMP3-expressing DCs, and T cells. As observed in skin lesions, serum levels of TNC and CCL18 were significantly elevated in AD and correlated with clinical disease severity.

overall_design:
  Spatial Transcriptomics (Visium Spatial Gene Expression; 10X Genomics) of human skin biopsy samples. 14 skin biopsy samples were collected from 7 atopic dermatitis patients, 1 from lesional and 1 from non-lesional skin per patient. In addition, 6 skin biopsy samples were collected from 6 healthy donors to serve as a control.

contributors:
  Mitamura, Yasutaka;Reiger, Matthias;Kim, Juno;Xiao, Yi;Zhakparov, Damir;Tan, Ge;Rinaldi, Arturo O;Baerenfaller, Katja;Akdis, Mübeccel;Brüggen, Marie-Charlotte;Brunner, Patrick M;Roqueiro, Damian;Traidl-Hoffmann, Claudia;Akdis, Cezmi A

citation:
  Mitamura, Yasutaka et al. “Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis.” Allergy vol. 78,8 (2023): 2215-2231. doi:10.1111/all.15781


dataset_id: STDS0000224
species: Homo sapiens
tissues: Brain
technologies: 10x Visium
disease: Brain cortex
submission_date: 2021-09-21 00:00:00
last_modified: 2023-08-10 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184510
platforms: Illumina HiSeq 2000
pmid: 37081484
has_paired: SCDS0000011
title:
  Spatial transcriptomics: The effect of consecutive slices data integration on accurate cell type annotation and clustering

summary:
  In 10X Genomics Visium Spatial Gene Expression (ST), the resolution for distinguishing neighboring cells can be improved using data integration with single-cell/single-nuclei transcriptomics profiles. Besides, depending on the cell type and tissue, nuclei size may vary significantly to an extent that it may exceed the thickness of tissue slices. This may jeopardize capturing full transcriptomics profile of single slice due to the improper/incomplete incision of nuclei during cryosectioning process and this may cause drawbacks in downstream analysis.   To monitor the probable consequences, we monitored the effect of consecutive slices data integration (CSDI) on improvement of cell type clustering and annotation through transferring cell labels from a single-nuclei transcriptomics dataset to ST. To do so, two consecutive slices from the orbitofrontal neocortex and temporal neocortex of two post mortem brain samples were obtained and their spatial transcriptomics profiles were retrieved using 10x Genomics Visium Spatial Gene Expression protocol.     Using CSDI, not only the number of identified clusters were increased and the inconsistency between the pattern of clusters in consecutive slices was resolved, but the layered-structure of gray matter was unveiled. Besides, only after CSDI the transferred annotations from single-nuclei transcriptomics to ST could match the microscopic results.  CSDI can improve the ST clustering and cell type annotation by providing the full signals coming from all cell types of single slice of tissue. The codes in R programming language are publicly available at https://github.com/ElyasMo/ST_snRNA-seq

overall_design:
  Four pairs of consecutive slices from Orbitofrontal and Temporal neocortex of post mortem brain samples

contributors:
  Mieczkowski, Jakub;Mohammadi, Elyas;Chojnowska, Katarzyna;Bieńkowski, Michał;Kostecka, Anna;Magdalena, Koczkowska;Michał, Żmijewski;Marcin, Jąkalski;Martin, Inglesson;Bradley, Hyman;Natalia,  Filipowicz;Paweł, Olszewski;Hanna, Davies;Justyna, Wierzbicka;Dumanski, Jan;Piotrowski, Arkadiusz

citation:
  Mohammadi, Elyas et al. “Size matters: the impact of nucleus size on results from spatial transcriptomics.” Journal of translational medicine vol. 21,1 270. 21 Apr. 2023, doi:10.1186/s12967-023-04129-z


dataset_id: STDS0000214
species: Mus musculus
tissues: Brain
sex: Female
technologies: 10x Visium
disease: Brain cortex
submission_date: 2022-11-22 00:00:00
last_modified: 2023-08-08 00:00:00
contributors: Mongrain, Valerie;Ballester Roig, Maria Neus;Dufort-Gervais, Julien
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218537
platforms: Illumina NovaSeq 6000
pmid: 37143153
title:
  Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics (additional files)

summary:
  Here, we investigated the effects of Rhynchophylline (RHY) on the mouse brain spatial transcriptome. More precisely, we injected male and female mice intraperitoneally with either saline (NaCl) or RHY, either at Zeitgeber time (ZT referring to time in hour after light onset) 0 or ZT0 and ZT11. Brains were sampled at ZT4 or ZT14, respectively, and immediately frozen embedded in OCT. Brains were treated and libraries were prepared according to 10x Genomics protocols for Visium Spatial Gene Expression. Sequencing was conducted by Genome Quebec (Montreal, Quebec, Canada). Findings reveal molecular routes by which RHY acts on the brain in a sleep-relevant context. Please cite the original paper when using these data (Ballester Roig et al., Biol Direct, 2023) and see also the submission GSE217058.

overall_design:
  Brain transcriptome measured 3 to 4 hours after one or two intraperitoneal injection of Rhynchophylline (RHY, 100 mg/kg) conducted at two different times of the day (ZT0 or ZT0 and ZT11) in male and female C57BL/6J mice that were kept under a 12 h light:12 h dark cycle. The same measurements were conducted in mice receiving saline (acting as controls). The total number of samples for this project is thus 8 (one female receiving RHY at ZT0, one female receiving saline at ZT0, one female receiving RHY at ZT0 and ZT11, one female receiving saline at ZT0 and ZT11, one male receiving RHY at ZT0, one male receiving saline at ZT0, one male receiving RHY at ZT0 and ZT11, one male receiving saline at ZT0 and ZT11). The brain transcriptome was quantified with the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics). Original fastq files and processed files were uploaded at GSE217058. However, raw fastq files for two samples were damaged during file storage and are missing (i.e., female receiving RHY at ZT0 and female receiving saline at ZT0 and ZT11). Here we provide the BAM files of these two samples (ZT4_F_RHY and ZT14_F_Saline) which were created with the pipeline ''spaceranger count'' with the original uncorrupted fastq files. These BAM files can be used to reconstitute the corresponding fastq files using the bamtofastq tool.

citation:
  Ballester Roig, Maria Neus et al. “Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics.” Biology direct vol. 18,1 21. 5 May. 2023, doi:10.1186/s13062-023-00377-7


dataset_id: STDS0000218
title: Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics
species: Mus musculus
tissues: Brain
sex: F/M
technologies: 10x Visium
disease: Brain cortex
submission_date: 2022-11-01 00:00:00
last_modified: 2023-08-08 00:00:00
contributors: Mongrain, Valerie;Ballester Roig, Maria Neus;Dufort-Gervais, Julien
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217058
platforms: Illumina NovaSeq 6000
pmid: 37143153
summary:
  Here, we investigated the effects of Rhynchophylline (RHY) on the mouse brain spatial transcriptome. More precisely, we injected male and female mice intraperitoneally with either saline (NaCl) or RHY, either at Zeitgeber time (ZT referring to time in hour after light onset) 0 or at ZT0 and ZT11. Brains were sampled at ZT4 or ZT14, respectively, and immediately frozen embedded in OCT. Brains were treated and libraries were prepared according to 10x Genomics protocols for Visium Spatial Gene Expression. Sequencing was conducted by Genome Quebec (Montreal, Quebec, Canada). Findings reveal molecular routes by which RHY acts on the brain in a sleep-relevant context. Please cite the original paper when using these data (Ballester Roig et al., Biol Direct, 2023).

overall_design:
  Brain transcriptiome measured 3 to 4 hours after one or two intraperitoneal injection of Rhynchophylline (RHY, 100 mg/kg) conducted at two different times of the day (ZT0 or ZT0 and ZT11) in male and female C57BL/6J mice that were kept under a 12 h light:12 h dark cycle. The same measurements were conducted in mice receiving saline (acting as controls). The total number of samples for this project is thus 8 (one female receiving RHY at ZT0, one female receiving saline at ZT0, one female receiving RHY at ZT0 and ZT11, one female receiving saline at ZT0 and ZT11, one male receiving RHY at ZT0, one male receiving saline at ZT0, one male receiving RHY at ZT0 and ZT11, one male receiving saline at ZT0 and ZT11). The brain transcriptome was quantified with the Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics).
  ***Please note that raw fastq files for two samples have been damaged during file storage and thus are not provided (female receiving RHY at ZT0 and female receiving saline at ZT0 and ZT11). BAM files of these two samples are provided in GSE218537.***

citation:
  Ballester Roig, Maria Neus et al. “Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics.” Biology direct vol. 18,1 21. 5 May. 2023, doi:10.1186/s13062-023-00377-7


dataset_id: STDS0000225
species: Homo sapiens
tissues: Pancreas
technologies: 10x Visium
disease: Pancreatic cancer
submission_date: 2022-06-02 00:00:00
last_modified: 2023-07-30 00:00:00
contributors: QIU, MENGJIE;Yousuf, Suhail;von Voithenberg, Lena V;Imbusch, Charles D;Roth, Susanne
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205354
platforms: NextSeq 550
pmid: 37263303
title:
  Spatially resolved multi-omics single-cell analyses inform mechanisms of immune-dysfunction in pancreatic cancer

summary:
  As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient survival. We substantiate the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlight immune subpopulations with potentially underappreciated roles in PDAC, particularly CD4 T cell subsets presenting immunosuppressive phenotypes with varying modes of exhaustion. We also demonstrate the dynamic changes associated with transcriptional reprogramming of immune subtypes within adjacent normal tissue and tumor surrounding stroma, and further reveal striking differences between immune phenotypes in PDAC and lung adenocarcinoma, which at least partially explain their differential responsiveness to current immunotherapies and might have implications for the development of novel treatment strategies.

overall_design:
  Eight tissue sections were subjected to spatial transcriptomic analysis by using the Visium technology(30) (10x Genomics) according to the protocol of the manufacturer. Briefly, tissue slices approximately 10um in size were cut from fresh frozen OCT embedded tissue sections and placed on the Visium slide. The tissue sections were lysed in situ on the slide, mRNA was released which was captured by the oligonucleotides attached to the slide. Double stranded cDNA was prepared and finally eluted out from the slide into a tube. cDNA was amplified, cleaned and a dual indexed library was prepared. The library was sequenced at the DKFZ sequencing core facility using a NextSeq platform. Cell types in different regions of the tissue sections were annotated by pathologists and the annotation was transferred to the spatial transcriptomic experiments in the array of spots.

citation:
  Yousuf, Suhail et al. “Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer.” Gastroenterology, S0016-5085(23)00810-7. 30 May. 2023, doi:10.1053/j.gastro.2023.05.036


dataset_id: STDS0000228
title: Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution
species: Mus musculus
tissues: Bone
organ_parts: Femur
development_stages: 3 months;18 months
technologies: GeoMx DSP
disease: Bone Marrow
submission_date: 2023-02-08 00:00:00
last_modified: 2023-07-27 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224838
platforms: Illumina NovaSeq 6000
pmid: 37255850
summary:
  Megakaryocytes are bone marrow (BM) resident cells that derive from hematopoietic stem cells. A pivotal function of megakaryocytes is the generation of platelets through the release of long protrusions called proplatelets into sinusoidal vessels. single-cell RNA-sequencing on murine BM megakaryocytes has previously revealed transcriptional heterogeneity with segmentation into four distinct categories. These studies postulated functions beyond platelet production with evidence for immunoregulatory and stem cell niche supporting subtypes, as well as a cycling population. The spatial context and transcriptional heterogeneity of megakaryocytes is of great interest as localization of for instance the vasculature is a necessity for platelet production. For single-cell RNA sequencing this spatial orientation is however lost due to the dissociation of tissues. Recent technological advances have enabled the interrogation of gene expression profiles of tissues in situ. This enables the integration of morphological, situational and transcriptional information to classify cells in the context of their microenvironment. In the following we present, for the first time, the application of this technology to BM megakaryocytes at a single cell level.

overall_design:
  The femur of a healthy 3 and 18 month old mice was collected and parafin sections were prepared. Using the Nanostring GeoMx spatial transcritomics platform individual megakaryocytes (guided by CD41 IF staining) were selected as regions of interest and their transcriptome was determined using the murine whole transcriptome atlas.

contributors:
  Billingsley, James M.;Stone, Andrew P;Tilburg, Julia;Scoville, David;Italiano, Joseph E;Billingsley, James M;Machlus, Kellie R

citation:
  Tilburg, Julia et al. “Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution.” Research and practice in thrombosis and haemostasis vol. 7,4 100158. 20 Apr. 2023, doi:10.1016/j.rpth.2023.100158


dataset_id: STDS0000217
title: Spatiotemporal multi-omics decoding of the developing human spinal cord
species: Homo sapiens
tissues: Spinal cord
technologies: 10x Visium
disease: Spin cord development
summary: This SuperSeries is composed of the SubSeries listed below.
submission_date: 2022-11-30 00:00:00
last_modified: 2023-07-27 00:00:00
contributors: Czarnewski, Paulo
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219122
platforms: Illumina NovaSeq 6000
pmid: 37095395
has_paired: STDS0000217
overall_design:
  Refer to individual Series

  Authors state "However, raw reads from our cohort are considered sensitive and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA."

citation:
  Li, Xiaofei et al. “Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.” Nature neuroscience vol. 26,5 (2023): 891-901. doi:10.1038/s41593-023-01312-9


dataset_id: STDS0000219
title: Spatial resolution of cellular senescence dynamics in colorectal liver metastasis
species: Homo sapiens
tissues: Liver
organ_parts: CRLM
technologies: 10x Visium
disease: Liver metastasis cancer
overall_design: Comparative spatial gene expression profiling of senescent cancer cells subpopulations
submission_date: 2022-06-21 00:00:00
last_modified: 2023-07-17 00:00:00
contributors: Faggioli, Francesca;Lambroia, Luca
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206552
platforms: NextSeq 550
pmid: 37157887
has_paired: SCDS0000006
summary:
  Heterogeneity of senescent cancer cells have been dissected by Spatial Transcriptomic in human colorectal liver metastasis (CRLM).

citation:
  Garbarino, Ombretta et al. “Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis.” Aging cell vol. 22,7 (2023): e13853. doi:10.1111/acel.13853


dataset_id: STDS0000221
title: Spatial transcriptomics of adenoid cystic carcinoma of the lacrimal gland
species: Homo sapiens
tissues: Eye
organ_parts: Adenoid cystic carcinoma of lacrimal gland
technologies: 10x Visium
disease: Adenoid cystic carcinoma of the lacrimal gland
submission_date: 2023-03-31 00:00:00
last_modified: 2023-07-06 00:00:00
contributors: Pelaez, Daniel;Moeyersoms, Acadia H
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228685
platforms: Illumina NovaSeq 6000
pmid: 37370820
has_paired: SCDS0000007
summary:
  We performed spatial transcriptomics of a tumor section from a patient post-treatment with adenoid cystic carcinoma of the lacrimal gland.

overall_design:
  LGACC tissue was embedded in paraffin at the time of excision. The FFPE block was sliced at 10 µm and placed on 10x Genomics Visium slide for spatial transcriptomic pipeline.

citation:
  Moeyersoms, Acadia H M et al. “Spatial Transcriptomics Identifies Expression Signatures Specific to Lacrimal Gland Adenoid Cystic Carcinoma Cells.” Cancers vol. 15,12 3211. 16 Jun. 2023, doi:10.3390/cancers15123211


dataset_id: STDS0000213
species: Homo sapiens
tissues: Kidney
development_stages: 16.6 GWA;6 years old;5 years old
sex: F/M
technologies: 10x Visium
disease: Wilms Tumors cancer
overall_design: Three total samples, one healthy fetal kidney and two Wilms tumor samples
submission_date: 2021-06-16 00:00:00
last_modified: 2023-07-01 00:00:00
contributors: Core, AGCT;Perin, Laura
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178349
platforms: Illumina NovaSeq 6000
pmid: 37114795
has_paired: STDS0000213
title:
  Transcriptome profiling between unfavorable and favorable Wilms Tumors and against human fetal kidney

summary:
  Purpose: The 10x Genomics Visium platform allows us to define the spatial topography of gene expression and provides detailed molecular maps that overcome limitations associated with sn/scRNA-seq and microscopy-based spatial transcriptomics methods. The goals of this study are to compare and identify unique transcriptome profiling (RNA-seq) signature between unfavorable and favorable Wilms Tumors and against human fetal kidney.
  Methods: Human fetal kidney and Wilms tumor spatial topography of gene expression were generated using the 10X Visium platform
  Results: Using an optimized data analysis workflow, we mapped the reads to the hg38 genome build and grouped the spots into 9 clusters based on gene expression profiles.
  Conclusion: Our study represents the first implement of Visium technology in human fetal kidney and Wilms Tumor tissue, providing a number of important functional insights about the spatial and molecular definitions of cell populations across human fetal kidney and different subtypes of Wilms Tumor through analyzing gene expression within the intact spatial organization of the human samples.

citation:
  Petrosyan, Astgik et al. “Identification and Characterization of the Wilms Tumor Cancer Stem Cell.” Advanced science (Weinheim, Baden-Wurttemberg, Germany) vol. 10,20 (2023): e2206787. doi:10.1002/advs.202206787


dataset_id: STDS0000204
title: Spatial transcriptomics (Visium, 10x Genomics) data of Duchenne mouse models
species: Mus musculus
tissues: Muscle
organ_parts: Skeletal muscle (quadriceps)
development_stages: 10 weeks
technologies: 10x Visium
disease: Nornal atlas
submission_date: 2022-03-29 00:00:00
last_modified: 2023-06-29 00:00:00
contacts: p.spitali@lumc.nl
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199659
platforms: Illumina NovaSeq 6000
pmid: 37582915
has_paired: SCDS0000003
summary:
  Quadricep sections of 10µm thick were placed on Visium spatial transcriptomics slide to obtain spatial datasets for these skeletal muscle sections

overall_design:
  healthy controls (C57BL10 and DBA/2J) and DMD affected mouse models (mdx and D2-mdx samples) all n=1

contributors:
  Spitali, Pietro;Heezen, Laura;Abdelaal, Tamim;van Putten, Maaike;Aartsma-Rus, Annemieke;Mahfouz, Ahmed

citation:
  Heezen LGM, Abdelaal T, van Putten M, Aartsma-Rus A et al. Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models. Nat Commun 2023 Aug 15;14(1):4909. 


dataset_id: STDS0000216
species: Homo sapiens
tissues: Colon;Liver
organ_parts: Colorectal tissue;Liver tissue
technologies: scRNA;10x Visium
disease: Liver metastasis cancer
submission_date: 2023-02-22 00:00:00
last_modified: 2023-06-16 00:00:00
contributors: Long, Jie;Wang, Fei
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225857
platforms: Illumina NovaSeq 6000
pmid: 37327339
has_paired: STDS0000216
title:
  Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer

summary:
  In this study, we comprehensively charted the cellular landscape of colorectal cancer (CRC) and well-matched liver metastatic CRC using single-cell and spatial transcriptome RNA sequencing. We generated 41892 CD45- non-immune cells and 196473 CD45+ immune cells from 27 samples of 6 CRC patients, and found that CD8_CXCL13 and CD4_CXCL13 subsets increased significantly in liver metastatic samples that exhibited high proliferation ability and tumor-activating characterization, contributing to better prognosis of patients. Distinct fibroblast profiles were observed in primary and liver metastatic tumors. The F3+ fibroblasts enriched in primary tumors contributed to worse overall survival by expressing pro-tumor factors. However, the MCAM+ fibroblasts enriched in liver metastatic tumors might promote generation of CD8_CXCL13 cells through Notch signaling. In summary, we extensively analyzed the transcriptional differences of cell atlas between primary and liver metastatic tumors of CRC by single-cell and spatial transcriptome RNA sequencing, providing different dimensions of the development of liver metastasis in CRC

overall_design:
  For single-cell RNA sequencing, 6 CRC patients with liver metastasis were enrolled after written informed consent was obtained. Primary CC, CN (at least 2 cm from matched tumors), LM, LN (at least 2 cm from matched tumors) and PB of the enrolled patients were collected following resection. All the patients received preoperative chemotherapy and/or radiotherapy. For spatial transcriptome sequencing, formalin-fixed paraffin embedded (FFPE) tissues of 6 CRC patients were prepared.

  Submitter states: Raw data are not included due to patient privacy concerns, which are deposited in the CNGB Nucleotide Sequence Archive (CNSA: https://db.cngb.org/cnsa; accession number: CNP0002540 for single cell RNA sequencing data, and CNP0003321 for spatial transcriptome RNA sequencing data)

citation:
  Wang, Fei et al. “Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer.” Science advances vol. 9,24 (2023): eadf5464. doi:10.1126/sciadv.adf5464


dataset_id: STDS0000189
species: Mus musculus
tissues: Brain
development_stages: 7 months
sex: Male
technologies: 10x Visium
disease: Brain Hypothalamus
submission_date: 2023-01-16 00:00:00
last_modified: 2023-05-31 00:00:00
contributors: Wu, Qiaofeng;Liu, Shuqing;Zhang, Ning;Li, Hongying
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222981
platforms: Illumina NovaSeq 6000
pmid: 36819717
has_paired: SCDS0000004
title:
  Moxibustion Improves Hypothalamus Aqp4 Polarization in APP/PS1 Mice: Evidence from Spatial Transcriptomics

summary:
  Aquaporin-4 (AQP4) is highly polarized to perivascular astrocytic endfeet. Loss of AQP4 polarization is associated with many diseases. In Alzheimer's disease (AD), it is found that AQP4 loos its normal location and thus reduce the clearance of amyloid-β plaques and Tau protein. Clinical and experimental studies show that moxibustion can improve the learning and memory abilities of AD. In order to explore whether moxibustion can affect the polarization of AQP4 around blood brain barrier (BBB), we used spatial transcriptomics (ST) to analyze the expression and polarization of Aqp4 in wild type mice, APP/PS1 mice and APP/PS1 mice intervened by moxibustion. The results showed that moxibustion improved the loss of abnormal polarization of AQP4 in APP/PS1 mice, especially in the hypothalamic BBB. Besides, there are other 31 genes with Aqp4 as the core have the similar depolarization in APP/PS1 mice, most of which are also membrane proteins. The majority of them have been reversed by moxibustion. At the same time, we employed the cerebrospinal fluid circulation gene set, which was found being on a higher level in the group of APP/PS1 mice with moxibustion treatment. Finally, in order to further explore its mechanism, we analyzed the mitochondrial respiratory chain complex enzymes closely related to energy metabolism, and found that moxibustion can significantly increase the expression of mitochondrial respiratory chain enzymes such as Cox6a2 in the hypothalamus, which could provide energy for mRNA transport. Our research shows that increasing the polarization of hypothalamic Aqp4 through mitochondrial energy supply may be an important target for moxibustion to improve APP/PS1 mice’s cognitive impairment.

overall_design:
  The WT mice were male C57BL/6J mice, while AD model mice were male APP/PS1 double transgenic mice. All the mice were screened by Morris water maze test after a week of adaptation. Then APP/PS1 mice were randomly divided into AD model group (APP/PS1) and moxibustion group (APP/PS1+MOX), C57BL/6J wild-type mice were used as control group (WT group). Spatial Transcriptomics were generated by deep sequencing, using Illumina NovaSeq 6000.

citation:
  Liu, Shuqing et al. “Moxibustion improves hypothalamus <i>Aqp4</i> polarization in APP/PS1 mice: Evidence from spatial transcriptomics.” Frontiers in aging neuroscience vol. 15 1069155. 2 Feb. 2023, doi:10.3389/fnagi.2023.1069155


dataset_id: STDS0000211
species: Homo sapiens
tissues: Brain
organ_parts: GBM Tissue;Human cell lines
development_stages: 64;65;53;54;33;41;63;71;25;22;68;61;30;59;70;58;48;42;43;69;23
sex: F/M
technologies: 10x Visium;snRNA;RNAseq
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2023-03-29 00:00:00
last_modified: 2023-05-24 00:00:00
contributors: Al Dalahmah, Osama
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228500
platforms: Illumina NextSeq 500;NextSeq 550;Illumina NovaSeq 6000
pmid: 37142563
title:
  Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states

disease:
  Primary | Recurrent | Cortex with astrogliosis | Focal architecture abnormalities; hippocampus with focal neuronal loss | Seizure epileptic brain

citation:
  Al-Dalahmah, Osama et al. “Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states.” Nature communications vol. 14,1 2586. 4 May. 2023, doi:10.1038/s41467-023-38186-1


dataset_id: STDS0000227
title: Spatial transcriptomics of de novo NEPC and ARPC
species: Homo sapiens
tissues: Prostate
organ_parts: Prostatic cancer
sex: Male
technologies: 10x Visium
disease: Prostatic cancer
overall_design: Formalin-fixed, paraffin-embedded (FFPE) samples of resected prostate specimen
submission_date: 2023-04-21 00:00:00
last_modified: 2023-05-21 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230282
platforms: DNBSEQ-G400
pmid: 37240308
has_paired: SCDS0000005
summary:
  We analyze and report the differences in gene expression between de novo NEPC and ARPC using spatial gene expression analysis techniques (Visium CytAssist, 10x genomics).

contributors:
  Motooka, Daisuke;Watanabe, Ryuta;Miura, Noriyoshi;Kurata, Mie;Kitazawa, Riko;Kikugawa, Tadahiko;Saika, Takashi

citation:
  Watanabe, Ryuta et al. “Spatial Gene Expression Analysis Reveals Characteristic Gene Expression Patterns of De Novo Neuroendocrine Prostate Cancer Coexisting with Androgen Receptor Pathway Prostate Cancer.” International journal of molecular sciences vol. 24,10 8955. 18 May. 2023, doi:10.3390/ijms24108955


dataset_id: STDS0000222
species: Homo sapiens
tissues: Colon
organ_parts: Primary colorectal cancer;CRLM
development_stages: 73;76;71;65;60;69;79
technologies: GeoMx DSP
disease: Primary colorectal cancer;CRLM
submission_date: 2023-02-01 00:00:00
last_modified: 2023-05-11 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224235
platforms: NanoString Human nCounter PanCancer IO 360 Panel
pmid: 37057593
title:
  Spatially Resolved Transcriptomics Deconvolutes Histological Prognostic Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases

summary:
  This bulk mRNA data was generated using the Nanostring ncounter platform using an io360 pancancer panel of 900 genes as part of a wider project which included spatial transcriptomic data generated using the Nanostring GeoMx platform.  In this study we compared tissue surgical resected from patients with colorectal cancer and liver metastases.

overall_design:
  We compered the matched primary and metastatic lesions.  The lesions were further annotated using histological scores to determine immune infiltration and stromal content, we further used these annotations to interrogate the mRNA data generated from nCounter

contributors:
  Wood, Colin;admin, GEO;Pennel, Kathryn;Leslie, Holly;Legrini, Assya;Cameron, Andrew J;Melissourgou-Syka, Lydia;Quinn, Jean A;van Wyk, Hester C;Hay, Jennifer;Roseweir, Antonia K;Nixon, Colin;Roxburgh, Campbell S;McMillan, Donald C;Biankin, Andrew V;Sansom, Owen J;Horgan, Paul G;Edwards, Joanne;Steele, Colin W;Jamieson, Nigel B

citation:
  Wood, Colin S et al. “Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases.” Cancer research vol. 83,8 (2023): 1329-1344. doi:10.1158/0008-5472.CAN-22-2794


dataset_id: STDS0000220
species: Homo sapiens
tissues: Pancreas
organ_parts: Donor pancreas;Primary PDAC tumor
technologies: GeoMx DSP
disease: Donor pancreas;Primary PDAC cancer
submission_date: 2023-03-07 00:00:00
last_modified: 2023-05-08 00:00:00
contributors: Pasca di Magliano, Marina
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226829
platforms: Illumina NovaSeq 6000
pmid: 37021392
title:
  Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early pre-neoplastic pancreatic lesions

summary:
  The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathological analysis of the samples revealed PanIN lesions in most individuals irrespective of age. Using a combination of multiplex immunohistochemistry, single cell RNA sequencing, and spatial transcriptomics, we provide the first ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts, and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis.

overall_design:
  A total of 4 slides containing 6 tissue sections (2 healthy pancreas, 4 tumor) was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) and immune cells (CD45), together with DAPI for nuclei detection. 277 ROIs were captured for whole transcriptome profiling.

citation:
  Carpenter, Eileen S et al. “Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions.” Cancer discovery vol. 13,6 (2023): 1324-1345. doi:10.1158/2159-8290.CD-23-0013


dataset_id: STDS0000215
title: Gene expression of human angiosarcoma
species: Homo sapiens
tissues: Tumor
organ_parts: Angiosarcomas
sex: F/M
technologies: GeoMx DSP
disease: Tumor metastasis
overall_design: A series of human angiosarcomas was profiled using the NanoString PanCancer IO 360 panel
submission_date: 2023-02-28 00:00:00
last_modified: 2023-05-04 00:00:00
contributors: Chan, Jason Yongsheng;admin, GEO;Chan, Jason
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226338
platforms: NanoString Human nCounter PanCancer IO 360 Panel
pmid: 37106027
development_stages:
  59;Non-metastatic;79;Non-metastatic;75;Non-metastatic;32;Non-metastatic;53;Non-metastatic;67;Non-metastatic;65;Non-metastatic;71;Metastatic;63;Non-metastatic;73;Metastatic;37;Non-metastatic;73;Non-metastatic;54;Metastatic;86;Non-metastatic;58;Non-metastatic;88;Non-metastatic;72;Metastatic;76;Non-metastatic;63;Metastatic;66;Non-metastatic;62;Metastatic;77;Metastatic;35;Non-metastatic;43;Non-metastatic;81;Non-metastatic;77;Non-metastatic;68;Non-metastatic;70;Non-metastatic;80;Non-metastatic;55;Metastatic;65;Metastatic;42;Metastatic;42;Non-metastatic;74;Metastatic;64;Metastatic;45;Non-metastatic;36;Non-metastatic;57;Non-metastatic;60;Non-metastatic;71;Non-metastatic;49;Metastatic;78;Non-metastatic;28;Non-metastatic;60;Metastatic;93;Unknown;78;Metastatic;85;Metastatic;62;Non-metastatic;76;Metastatic;66;Metastatic

summary:
  Gene expression profiling of human angiosarcoma samples was performed using the NanoString Human nCounter PanCancer IO 360 Panel

citation:
  Loh, Jui Wan et al. “Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.” Communications biology vol. 6,1 461. 27 Apr. 2023, doi:10.1038/s42003-023-04856-5


dataset_id: STDS0000226
title: Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma
species: Homo sapiens
tissues: Blood vessel
organ_parts: Angiosarcomas
technologies: 10x Visium
disease: Head and neck angiosarcoma
overall_design:
  Spatial transcriptomics of 4 Asian Head and Neck Angiosarcoma
  10X Genomics Visium

submission_date: 2023-03-16 00:00:00
last_modified: 2023-05-03 00:00:00
contributors: Lim, Abner;Chan, Yong-Sheng J;Loh, Jui W;Lim, Abner H
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227469
platforms: Illumina NovaSeq 6000
pmid: 37106027
summary:
  Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In this dataset spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in “immune-hot” cases and immune foci even in otherwise “cold” cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.

citation:
  Loh, Jui Wan et al. “Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.” Communications biology vol. 6,1 461. 27 Apr. 2023, doi:10.1038/s42003-023-04856-5


dataset_id: STDS0000184
title: Spatial transcriptomics on human lumbar spinal cord
species: Homo sapiens
tissues: Spinal cord
organ_parts: Lumbar spinal cord (L3/L4);Lumbar spinal cord (L5/S1)
technologies: 10x Visium
disease: Lumbar spinal cord
overall_design: Spatial transcriptomics using the 10x Genomics Visium array, on 20 sections from 4 donors
submission_date: 2023-01-06 00:00:00
last_modified: 2023-05-02 00:00:00
contributors: Menon, Vilas;Levine, Ariel J
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222322
platforms: Illumina HiSeq 3000
pmid: 36731429
summary:
  This study includes spatial transcriptomics on the human lumbar spinal cord using the 10x Genomics Visium platform. Frozen sections of spinal cord were placed on Visium slide arrays and processed using the 10x Genomics workflow, followed by alignment and quantification using the spaceranger package.

citation:
  Yadav, Archana et al. “A cellular taxonomy of the adult human spinal cord.” Neuron vol. 111,3 (2023): 328-344.e7. doi:10.1016/j.neuron.2023.01.007


dataset_id: STDS0000229
species: Mus musculus
tissues: Heart
technologies: 10x Visium
disease: Myocardial Ischemia-Reperfusion Injury
submission_date: 2023-03-13 00:00:00
last_modified: 2023-04-29 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227238
platforms: Illumina NovaSeq 6000
pmid: 37229263
title:
  Single-nucleus Ribonucleic Acid-sequencing and Spatial Transcriptomics Reveal the Cardioprotection of Shexiang Baoxin Pill (MUSKARDIA) in Mice with Myocardial Ischemia-Reperfusion Injury

summary:
  The Shexiang Baoxin Pill (MUSKARDIA) has been extensively used to treat cardiovascular diseases in China for four decades, and its clinical efficacy has been widely approved. However, the mechanism by which this is achieved remains largely unexplored. Research attempting to understand the underlying mechanism is ongoing, but the findings are controversial. Here, we aimed to explore the possible mechanism of MUSKARDIA in myocardial ischemia-reperfusion (I/R) injury using heart single-nucleus and spatial ribonucleic acid (RNA) sequencing.

overall_design:
  Heart tissues of C57BL/6 mice were isolated from sham, I/R, and MUSKARDIA groups and analyzed using scRNAseq.

contributors:
  Lin, Wenyong;Chen, Xin;Wang, Dongyuan;Lu, Ruixia;Zhang, Chunling;Niu, Zhenchao;Chen, Jie;Ruan, Xiaofen;Wang, Xiaolong

citation:
  Lin, Wenyong et al. “Single-nucleus ribonucleic acid-sequencing and spatial transcriptomics reveal the cardioprotection of Shexiang Baoxin Pill (SBP) in mice with myocardial ischemia-reperfusion injury.” Frontiers in pharmacology vol. 14 1173649. 9 May. 2023, doi:10.3389/fphar.2023.1173649


dataset_id: STDS0000208
species: Mus musculus
tissues: Muscle
technologies: 10x Visium
disease: Normal atlas
submission_date: 2022-03-14 00:00:00
last_modified: 2023-04-20 00:00:00
contributors: Giordani, Lorenzo;Giodani, Lorenzo;D'Ercole, Chiara;Madaro, Luca
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198596
platforms: Illumina NovaSeq 6000
pmid: 36543136
title:
  Spatially resolved transcriptomics reveals innervation-responsive functional cluster in skeletal muscle.

summary:
  Striated muscle is a highly organized structure composed by well-defined anatomical domains with integrated but distinct assignments. Indeed, the lack of a direct correlation between tissue architecture and gene expression has thus far limited our understanding of how each unit responds to physio-pathologic contexts.  Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we followed the changes in the transcriptomics profile of specific domains in muscle in a model of denervation. Furthermore, our approach allowed us to identify the spatial distribution and nerve dependence of atrophic signalling pathway and polyamine metabolism to glycolytic fibres. Indeed, we demonstrate a pronounced alteration of polyamine homeostasis upon denervation.

overall_design:
  Spatial Transcriptomics analysis of wildtype murine Tibialis Anterior and Extensor digitorum longus prior and after Nerve Crush  (3 days  and 30 days )

citation:
  D'Ercole, Chiara et al. “Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle.” Cell reports vol. 41,12 (2022): 111861. doi:10.1016/j.celrep.2022.111861


dataset_id: STDS0000193
title: Spatial epigenome-transcriptome co-profiling of mammalian tissues
species: Homo sapiens;Mus musculus
tissues: Brain;Eymbro
organ_parts: Brain;Embryo;Hippocampus
technologies: CUT&Tag
disease: Normal atlas
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2022-05-29 00:00:00
last_modified: 2023-04-14 00:00:00
contributors: Zhang, Di
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205055
platforms: Illumina NovaSeq 6000;Illumina NovaSeq 6000
pmid: 36922587
citation:
  Zhang, Di et al. “Spatial epigenome-transcriptome co-profiling of mammalian tissues.” Nature vol. 616,7955 (2023): 113-122. doi:10.1038/s41586-023-05795-1


dataset_id: STDS0000207
species: Mus musculus
tissues: Ileum;Heart
technologies: scRNA;10x Visium
disease: Heart failure
submission_date: 2021-11-26 00:00:00
last_modified: 2023-04-13 00:00:00
contributors: De Vlaminck, Iwijn;Mantri, Madhav;Hinchman, Meleana M;Parker, John L
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189636
platforms: Illumina NextSeq 500;Illumina MiniSeq;NextSeq 2000
pmid: 36970396
title:
  Time-course single-cell and spatial transcriptomics of reovirus-induced myocarditis in neonatal mice

summary:
  A significant fraction of sudden death in young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used single-cell and spatially resolved RNA sequencing (RNA-seq) to study the cellular and spatial  heterogeneity of myocarditic processes in the hearts of reovirus-infected neonatal mice at multiple predetermined time points after initial infection at the primary site of infection. We further applied these technologies to study the innate response to reovirus infection in the intestine. In addition, we performed time-dependent single-cell RNA-seq (scRNA-seq) of cardiac tissues of mice infected with a reovirus point mutant that does not cause myocarditis. To establish viral tropism, we implemented molecular enrichment of non-polyadenylated viral transcripts that were otherwise poorly represented in the transcriptomes. Our measurements give insight into the cardiac cell-type specificity of innate immune responses, into the tropism of the virus in the intestine and the heart, into the transcriptional states of cell types involved in the production of inflammatory cytokines and the recruitment of circulating immune cells, and into the cell type specific gene expression in a spatial context. Overall, our data identify cellular interactions and cell-type specific host responses during reovirus-induced myocarditis.

overall_design:
  Time-course single-cell and spatial transcriptomics of ileum and heart tissues from reovirus-infected neonatal mice

citation:
  Mantri, Madhav et al. “Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.” Nature cardiovascular research vol. 1,10 (2022): 946-960. doi:10.1038/s44161-022-00138-1


dataset_id: STDS0000170
species: Homo sapiens
tissues: Cervical
organ_parts: Cervical tissue
technologies: Spatial Transcriptomics
disease: HPV
submission_date: 2022-07-20 00:00:00
last_modified: 2023-04-03 00:00:00
contributors: Guo, Chenyan
contacts: 13301050323@fudan.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208654
platforms: Illumina NovaSeq 6000
pmid: 36967539
has_paired: STDS0000170
title:
  Spatiotemporally Deciphering the Unknown Role of Persistent HPV Infection in Precancer to Cervical Cancer Progression: Integrating Single-Cell RNA-Sequencing Landscape and Spatial Transcriptomics Atlas [Spatial Transcriptomics]

summary:
  The mechanism underlying the cervical carcinogenesis mediated by persistent HPV infection remains elusive. Here we pioneeringly deciphered both temporal transition and spatial distribution of the cellular subsets during the disease progression from normal cervix, precancer lesions to cervical cancer by integrating scRNA-seq with ST. We not only identified three ‘HPV-related epithelial clusters’ unique to normal, HSIL and cervical cancer respectively, but also discovered node genes which potentially determined the disease progression. Moreover, we observed a gradual transition of multiple immune cells from positive immune response to dysregulation and exhaustion, to an immune-suppressive microenvironment during the malignant program. Besides, the cellular interaction analysis further verified a ‘homeostasis-balance-malignancy’ change within cervix microenvironment during disease escalation. Together, these findings not only deciphered mysterious persistent HPV infection spatiotemporally from the process of precancer to cervical cancer but also provided unprecedented possibilities for accurate diagnosis, precise treatment and prognosis evaluation for precancer and cervical cancer.

overall_design:
  Nine cervical tissue samples of different disease stages from normal, HPV-infected, precancer to cancer were collected from colposcopy examination and analyzed using scRNAseq and spatial transcriptomics .

citation:
  Guo, Chenyan et al. “Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome.” Clinical and translational medicine vol. 13,3 (2023): e1219. doi:10.1002/ctm2.1219


dataset_id: STDS0000201
species: Mus musculus
tissues: Brain
sex: Male
technologies: 10x Visium
disease: Secondary Brain Injury
submission_date: 2022-09-28 00:00:00
last_modified: 2023-03-15 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE214349
platforms: Illumina NovaSeq 6000
pmid: 36825001
has_paired: SCDS0000008
title:
  Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis

summary:
  Intraventricular haemorrhage (IVH) is one of the common complications after various acute brain injuries, leading to severe mortality and mobility, with great burdens on economics and society. Recently, a CLEAR III trial (NCT00784134) employing alteplase effectively cleared intraventricular haematoma but did not demonstrate adequate neuro behavioural benefits for patients. Therefore, the present study sought to investigate the pathophysiology of how these haematoma stimulations in ventricles cause neurological dysfunction. An autologous blood stereotactic injection model was employed to establish and mimic secondary IVH in mice, followed by our innovated spatial transcriptome sequencing-based bioinformatic algorithm to investigate the 3D spatial brain regions affected by the primary stimulation of haematoma in the ipsilateral ventricle after IVH, as well as related cell-cell communication strength and pathway analysis. These data illustrate that the three main 3D global pseudospace-time trajectory bundles represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. To the best of our knowledge, this is the first study to interrogate secondary brain injury after IVH by using spatial transcriptome sequencing and bioinformatics analysis. These data could provide more helpful information on the pathophysiological mechanism of IVH in patients after acute brain injury, as well as for the bioinformatics analysis strategies for similar studies in the future.

overall_design:
  We collected wild-type C57/BL6 mouse brains, which were classified into the no-surgery group (control), the needle-puncture group without blood injection (sham), and the needle-puncture group with blood injection at 1st, 3rd and 7th day. Then, these brains were frozen on dry ice in OCT.Frozen brains were then sectioned coronally at 10 μm on a cryostat and mounted on 10x Genomics Visium spatial transcriptome slides. The tissue locations of the library patches started from the emergence of the lateral ventricle with 20 μm intervals and a 10 μm margin of error.

contributors:
  Badai, Jiayidaer;Zhang, Le;Wang, Guan;Ru, Xufang;Song, Wenkai;You, Yujie;He, Jiaojiao;Huang, Suna;Feng, Hua;Chen, Runsheng;Zhao, Yi;Chen, Yujie

citation:
  Zhang, Le et al. “Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis.” Frontiers in immunology vol. 14 1123652. 7 Feb. 2023, doi:10.3389/fimmu.2023.1123652


dataset_id: STDS0000206
species: Homo sapiens
tissues: Neuron
technologies: 10x Visium
disease: pediatric and adult malignant gliomas
submission_date: 2022-01-25 00:00:00
last_modified: 2023-03-14 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194329
platforms: Illumina HiSeq 2000
pmid: 36823172
title:
  Spatial multi-omics reveals vulnerabilities of radial glia-like cancer-initiating cells within distinct ecosystems of pediatric and adult malignant gliomas

summary:
  We collected five DMG, five GBM (including two secondary GBM), and one peritumor samples from eleven patients requiring surgical resection. To establish an atlas for spatially-resolved gene expression, we performed short-read  spatial transcriptomic sequencing  on the tissue sections using the 10x Visium platform.

overall_design:
  Here, we established a spatial atlas of H3K27M-DMG and GBM through short read spatial transcriptomics to reveal the niche-specific distribution and vulnerability of stem-like cells in H3K27M-DMG and GBM

contributors:
  Wang, Yuan;Huang, Zongyao;Ren, Yanming;Zhou, Lingling;Xiao, Peng;Song, Junwei;Chen, Lu;Ju, Yan;Zhang, Yuekang

citation:
  Ren, Yanming et al. “Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas.” Nature communications vol. 14,1 1028. 23 Feb. 2023, doi:10.1038/s41467-023-36707-6


dataset_id: STDS0000173
species: Mus musculus
tissues: Muscle
development_stages: 6 months;11 days
sex: F/M
technologies: 10x Visium
disease: Hindlimb muscle regeneration
submission_date: 2022-04-08 00:00:00
last_modified: 2023-03-05 00:00:00
contributors: McKellar, David William;McKellar, David W;Mantri, Madhav;De Vlaminck, Iwijn;Cosgrove, Benjamin D
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200481
platforms: Illumina NextSeq 500;NextSeq 2000
pmid: 36329320
title:
  Spatial Total RNA-Sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart

summary:
  Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying endogenously polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNAs enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We apply this Spatial Total RNA-Sequencing (STRS) approach to spatially map noncoding RNAs, newly transcribed RNAs, and non-host RNAs at the tissue-scale in the study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify noncoding transcripts which exhibit zonal variation in skeletal muscle regeneration, and highlight host transcriptional responses highly associated with local viral RNA abundance. Our in situ polyadenylation strategy relies on a brief, low-cost add-on to a widely used protocol for spatial RNA-sequencing, and thus could be broadly and quickly adopted. Spatial RNA-sequencing of the total transcriptome will enable new insights into spatial gene regulation and biology.

overall_design:
  Spatial total RNA-sequencing was performed using a modified version of the Visium protocol. After dissection, tissues were embedded in OCT compound and frozen fresh in liquid nitrogen. 10um thick tissue sections were mounted onto the Visium Spatial Gene Expression v1 slides. For heart samples, one tissue section was placed into each 6x6mm capture area. For skeletal muscle samples, two tibialis anterior sections were placed into each capture area. After sectioning, tissue sections were fixed in methanol for 20 minutes at -20oC. Next, H&E staining was performed according to the Visium protocol, and tissue sections were imaged. After imaging, the slide was placed into the Visium Slide Cassette. In situ polyadenylation was then performed using yeast Poly(A) Polymerase (Thermo Scientific, cat #74225Z25KU). First, samples were equilibrated by adding 100ul of 1X wash buffer (20ul 5X yPAP Reaction Buffer, 2ul 40U/ul Protector RNase Inhibitor, 78ul nuclease-free H2O) to each capture area and incubating at room temperature for 30 seconds. The buffer was then removed. Next, 75ul of yPAP enzyme mix (15ul 5X yPAP Reaction Buffer, 3ul of 600U/ul yPAP enzyme, 1.5ul 25mM ATP, 3ul 40U/ul Protector RNase Inhibitor, 52.5ul nuclease-free H2O) was added to each reaction chamber. The reaction chambers were then sealed and the slide cassette was incubated at 37oC for 25 minutes. The enzyme mix was then removed. Prior to running STRS, optimal tissue permeabilization time for both heart and skeletal muscle samples was determined to be 15 minutes using the Visium TIssue Optimization Kit from 10x Genomics. Following in situ polyadenylation, the standard Visium library preparation was followed to generate cDNA and final sequencing libraries. The libraries were then pooled and sequenced according to guidelines in the Visium Spatial Gene Expression protocol using either a NextSeq 500 or NextSeq 2000.

citation:
  McKellar, David W et al. “Spatial mapping of the total transcriptome by in situ polyadenylation.” Nature biotechnology vol. 41,4 (2023): 513-520. doi:10.1038/s41587-022-01517-6


dataset_id: STDS0000187
title: Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues
species: Homo sapiens;Mus musculus
tissues: Kidney;Lung
organ_parts: Kidney organoid;Lung organoid;Hippocampus
technologies: 10x Visium
disease: Nornal atlas
overall_design: Whole-genome transcriptomic profiling of formalin-fixed tissue sections
submission_date: 2021-10-12 00:00:00
last_modified: 2023-03-02 00:00:00
contributors: Larsson, Ludvig Ale;Ludvig, Larsson;Eva Gracia, Villacampa
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185715
platforms: NextSeq 2000;NextSeq 2000
pmid: 36776149
summary:
  Method to perform spatial analysis of mRNA in FFPE and PFA fixed tissue sections using spatially barcoded slides and based on oligo(dT) mRNA capture.

citation:
  Gracia Villacampa, Eva et al. “Genome-wide spatial expression profiling in formalin-fixed tissues.” Cell genomics vol. 1,3 100065. 8 Dec. 2021, doi:10.1016/j.xgen.2021.100065


dataset_id: STDS0000179
species: Mus musculus
tissues: Liver
technologies: GeoMx DSP
disease: Hepatic ischemia-reperfusion
submission_date: 2022-11-14 00:00:00
last_modified: 2023-02-26 00:00:00
contributors: Xin, Jiaqi;Yang, Ting;Wu, Xiaoyi;Wu, Yingting;Liu, Yi;Liu, Xuan;Jiang, Mengxi;Gao, Wei
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217936
platforms: Illumina NovaSeq 6000
pmid: 36804628
title:
  Gene expression profiles of mouse ischemia-reperfusion liver zones with or without celastrol-treated.

summary:
  Hepatic ischemia-reperfusion (I/R) has long affected the success rate of liver transplant. Though zone-specific injury induced by I/R was observed, elaborated cellular and molecular mechanisms underlying the I/R injury pattern have not been revealed. Spatial transcriptomics analysis has great potential to uncover the mechanisms of liver I/R injury.

overall_design:
  We evaluated the gene expression profile of different zones of mouse liver from sham group, 70% liver I/R group and celastrol-treated I/R group using DSP spatial transcriptomics analysis. 147 ROIs were sequenced totally.

citation:
  Xin, Jiaqi et al. “Spatial transcriptomics analysis of zone-dependent hepatic ischemia-reperfusion injury murine model.” Communications biology vol. 6,1 194. 18 Feb. 2023, doi:10.1038/s42003-023-04564-0


dataset_id: STDS0000180
title: Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss
species: Mus musculus;Canis lupus familiaris
tissues: Muscle
organ_parts: Skeletal Muscle
sex: F/M
technologies: 10x Visium
disease: Muscle regeneration
submission_date: 2022-06-08 00:00:00
last_modified: 2023-02-24 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205707
platforms: Illumina NovaSeq 6000;Illumina NovaSeq 6000
pmid: 36821376
summary:
  Volumetric muscle loss (VML) is an acute trauma that results in persistent inflammation, supplantation of muscle tissue with fibrotic scarring, and decreased muscle function. The cell types, nature of cellular communication, and tissue locations that drive the aberrant VML response have remained elusive. Herein, we used spatial transcriptomics on mouse and canine models of VML and observed VML engenders a unique spatial pro-fibrotic pattern driven by crosstalk between fibrotic and inflammatory macrophages and mesenchymal derived cells. The dysregulated response was conserved between murine and canine VML models, albeit with varying kinetics, and impinged on muscle stem cell mediated repair. Targeting this circuit in a murine model resulted in increased regeneration and reductions in inflammation and fibrosis. Collectively, these results enhance our understanding of the cellular crosstalk that drives aberrant regeneration and provides further insight into possible avenues for fibrotic therapy exploration.

overall_design:
  Spatial gene expression profiling was performed on flash-frozen, OCT embedded muscle tissue from mouse and canine post VML injury. Canine tissues were collected from two animals in different wound locations for a total of three spatial samples. Four replicates were generated for each treatment in mice (vehicle and ITD1) at 7 days post injury, and two replicates were generated for 14 days post injury.

contributors:
  Aguilar, Carlos Andres;Larouche, Jacqueline A;Wallace, Emily C;Spence, Bonnie D;Johnson, Scott A;Kulkarni, Mangesh;Buras, Eric;Brown, Bryan N;Badylak, Stephen F;Aguilar, Carlos A

citation:
  Larouche, Jacqueline A et al. “Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss.” JCI insight vol. 8,7 e162835. 10 Apr. 2023, doi:10.1172/jci.insight.162835


dataset_id: STDS0000185
title: Spatial transcriptomics of post-mortem lung tissue from COVID-19 donors
species: Homo sapiens
tissues: Lung
technologies: 10x Visium
disease: COVID-19
submission_date: 2021-12-12 00:00:00
last_modified: 2023-02-12 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190732
platforms: NextSeq 550
pmid: 36774347
summary:
  Visualization of gene expression in lung tissue was performed using Visium spatial gene expression kits (10x Genomics) following the manufacturer`s protocol. The four capture areas in a 10x Genomics Visium Gene Expression slide consist of 5000 spots with DNA oligos for mRNA capture that have a unique spatial barcode and a unique Molecular Identifier (UMI). Each spot has 55 µm diameter and can therefore capture mRNA from 1 to 10 cells. We report the spatially resolved transcriptome of 3 control lung samples from non-COVID-19-related pneumonia donors and 9 COVID-19 lung samples analyzed with the 10x Visium platform.

overall_design:
  Control (n=3) and COVID-19 lung samples (n=9) from donors categorized based on disease durations (acute n=3, chronic n=3, prolonged n=3) were cut into 10μm sections using a MH560, cryotome (ThermoFisher, Waltham, Massachusetts, USA), and mounted on 10X Visium slides, which were pre-cooled to −20°C. The sections were fixed in pre-chilled methanol for 30 min, stained with CD45-AF647, CD31-AF594 and DAPI for 30min and imaged using an LSM 880 confocal microscope (Zeiss). The sections were then permeabilized for 10 minutes and spatially tagged cDNA libraries were constructed using the 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit. Tissue sections from the same fresh frozen human lung samples used for MELC and snRNA-seq were analyzed by ST.

contributors:
  Hauser, Anja Erika;Pascual-Reguant, Anna;Liebeskind, Juliane;Köhler, Ralf;Mothes, Ronja;Hauser, Anja E

citation:
  Mothes, Ronja et al. “Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19.” Nature communications vol. 14,1 791. 11 Feb. 2023, doi:10.1038/s41467-023-36333-2


dataset_id: STDS0000183
title: Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
species: Mus musculus
tissues: Brain
organ_parts: Bone;Bartilage;Brain
development_stages: P4;P11;Young mice
technologies: 10x Visium
disease: Normal atlas
submission_date: 2022-12-22 00:00:00
last_modified: 2023-02-10 00:00:00
contributors: Larsson, Ludvig Ale;Andrusivova, Zaneta;Larsson, Ludvig;Mirzazadeh, Reza
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221571
platforms: NextSeq 2000
pmid: 36720873
summary:
  Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), an SRT workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we demonstrate the RRST protocol on tissue sections collected from five challenging tissue types, including: human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyzed 52 tissue sections and our results demonstrate that RRST is a versatile, powerful, and reproducible protocol for FF specimens of different qualities and origins.

overall_design:
  Gene expression profiiles of spatially resolved transcriptomics data generated from degraded or challenging samples

citation:
  Mirzazadeh, Reza et al. “Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.” Nature communications vol. 14,1 509. 31 Jan. 2023, doi:10.1038/s41467-023-36071-5


dataset_id: STDS0000209
title: Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection
species: Homo sapiens
tissues: Thymus;Blood
development_stages: 7 days;2.5 months;9 months;1.6 months;13.5 months;5 months;10 days;4 months;5.5 months;12 months
sex: F/M
technologies: scRNA;10x Visium
disease: T agonist
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2022-06-29 00:00:00
last_modified: 2023-02-10 00:00:00
contributors: Lie, Benedicte Alexandra
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207206
platforms: Illumina NovaSeq 6000
pmid: 36741401
has_paired: STDS0000209
citation:
  Heimli, Marte et al. “Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection.” Frontiers in immunology vol. 13 1092028. 20 Jan. 2023, doi:10.3389/fimmu.2022.1092028


dataset_id: STDS0000210
title: Mapping the Spatial Dynamics of the Human Oral Mucosa in Chronic Inflammatory Disease
species: Homo sapiens
tissues: Mucosa
organ_parts: Oral mucosa
technologies: 10x Visium
disease: Chronic Inflammatory Disease
submission_date: 2022-06-22 00:00:00
last_modified: 2023-02-02 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206621
platforms: Illumina NextSeq 500
pmid: 36648332
summary:
  The interplay among different cells in a tissue is essential for maintaining homeostasis. Although, disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies.  We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence in situ hybridisation to characterise human oral mucosa in health and oral chronic inflammatory disease. We define highly specialised epithelial and stromal compartments and describe location-specific immune programs. Furthermore, we discovered fine regional fibroblast states, and spatially mapped a rare pathogenic population localised in a highly immunogenic region, responsible for lymphocyte recruitment through CXCL8 and CXCL10 and with a possible role in pathological angiogenesis through ALOX5AP. Collectively, our study provides a comprehensive reference for the study of oral chronic disease pathogenesis.

overall_design:
  Adult oral mucosa tissue sections from healthy and periodontitis affected individuals were subjected to spatial transcriptomics analyses.

contributors:
  Sharpe, Paul;Caetano, A J;Redhead, Y;Karim, F;Dhami, P;Kannambath, S;Nuamah, R;Volponi, A A;Nibali, L;Booth, V;D'Agostino, E M;Sharpe, P T

citation:
  Caetano, Ana J et al. “Spatially resolved transcriptomics reveals pro-inflammatory fibroblast involved in lymphocyte recruitment through CXCL8 and CXCL10.” eLife vol. 12 e81525. 17 Jan. 2023, doi:10.7554/eLife.81525


dataset_id: STDS0000191
title: Spatial transcriptomic characterization of the lung parenchyma during COVID-19 pneumonitis
species: Homo sapiens
tissues: Lung
organ_parts: Postmortem Lung
technologies: GeoMx DSP
disease: COVID-19
submission_date: 2021-10-20 00:00:00
last_modified: 2023-01-30 00:00:00
contributors: Cross, Amy Rachael;Cross, A R;Sansom, S N;Issa, F
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186213
platforms: NextSeq 2000
pmid: 36472908
summary:
  Severe lung damage in COVID-19 is known to involve complex interactions between diverse populations of immune and stromal cells. The pneumonitis manifesting in COVID-19 and acute respiratory distress syndrome results in spatially heterogenous manifestations of injury, such as infiltrates, loss of epithelial integrity and fibrosis. In this study, we applied a spatial transcriptomics approach to better delineate the cells, pathways and genes responsible for promoting and perpetuating severe tissue pathology in COVID-19 pneumonitis. Guided by tissue histology and multiplex immunofluorescence, we performed a targeted sampling of dozens of regions representing a spectrum of diffuse alveolar damage (mild to severe) from the post-mortem lung of three COVID-19 patients.  These microscopic sites of injury had varying known compositions of CD3+ lymphocytes, CD68+ myeloid cells and panCK+ epithelial cells.
  DCC files are the processed sequencing files using the NanoString DND pipeline. The "Initial Dataset.xlsx" is represents raw gene counts for each probe replicate (n=47). "Post Biological Probe QC.xlsx" removes a sample (n=46) with failed sequencing (no rawReads) and conducts biological probe quality controls to collapse probe replicates into a single count per target gene using the GeoMx Analysis suite (version 2.1.0.102).  "qn.exprs.tsv" is the matrix of quantile normalised gene expression by segment (n=46) and  "qn.exprs.corrected.tsv" is the matrix of quantile normalised and batch corrected matrix of gene expression by segment (n=46). Rendered multichannel immunofluorescent microscopy png images corresponding to each area of interest (AOI with the acquistion borders outlined in white) are included.  Further images can be made available upon request.

overall_design:
  RNA expression was assessed in selected areas within the lung parenchyma from three COVID-19 patients. Tissues were obtained rapidly postmortem, through open biopsy. At least, 14 spatially distinct areas (AOI) per tissue section were sampled to demonstrate the breadth of inflammation and injury within the alveolar region (total AOI = 46).  The areas (AOI) were classified by the severity of alveolar tissue and the presence of proximal SARS-CoV-2 nucelocapsid in aligned non-sequential tissue sections.   These microscopic sites of injury had varying known compositions of CD3+ lymphocytes, CD68+ myeloid cells and panCK+ epithelial cells. The genes measured were included in the NanoString Cancer Transcriptome Atlas (CTA) panel and those included in the COVID-19 spike-in gene panel for added respiratory-related and SARS-CoV-2 genes. The raw count matrix, the quantile normalized expression matrix and the metadata (including the calculated CD3+ and CD68+ cell composition, and the severity of alveolar damage) are provided.  The corresponding immunofluorescence images of each AOI and the whole tissue scan can be provided upon request.

citation:
  Cross, Amy R et al. “Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury.” JCI insight vol. 8,2 e157837. 24 Jan. 2023, doi:10.1172/jci.insight.157837


dataset_id: STDS0000199
species: Homo sapiens
tissues: Lung
development_stages: 8.5 PCW;6 PCW;8 PCW;5 PCW;12 PCW;13 PCW;14 PCW;11.5 PCW;10 PCW;7 PCW;5.5 PCW
sex: F/M
technologies: 10x Visium
disease: Lung development
submission_date: 2022-10-17 00:00:00
last_modified: 2023-01-20 00:00:00
contributors: Czarnewski, Paulo;Sergio, Marco S;Alexandros, Sountoulidis;Paulo, Czarnewski;Christos, Samakovlis
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215895
platforms: NextSeq 2000
pmid: 36646791
title:
  A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [SC]

summary:
  The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here, we report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programs, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell-types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

overall_design:
  For tissue dissociation, tracheas were removed and lungs were finely minced. For later timepoints, lobes were first dissected into smaller pieces. Then, they were digested in 4U/ml Elastase (Worthington, cat no. LS002292), 1 mg/ml of DNase (Worthington, cat no. LK003170) in HBSS (Gibco, cat no. 14170) at 37°C ranging between 30 min to 3 h depending on the age (older timepoints require longer digestion times). HBSS supplemented with 2 % FCS (Gibco, cat no. 10500064) was used for the whole procedure. The tissues were triturated with fire polished glass Pasteur pipettes every 15-20 min for the tissue to fall apart more easily and enhance the dissociation. After digestion, the cell suspension was filtered (twice if needed) in a 15ml Falcon tube using a 30μm cell strainer (CellTrics, Sysmex), to remove remaining undissociated clumps and debris. The filtered cell suspension was kept ice cold and was diluted (roughly 1:2) with ice cold HBSS to prevent further digestion by the enzyme.. The filtered cell suspension wascells were pelleted through centrifugation at 200g for 5 min at 4 °C, the supernatant was removed and the pellet resuspended in a small volume of calcium- and magnesium-free HBSS (Gibco, cat no.14170) and transferred to 1.5ml Eppendorf tubes precoated with 30% BSA (A9576, Sigma-Aldrich). A Bürker chamber was used for cell counting.
  NOTE FROM SUBMITTER: raw reads from our cohort are considered sensate and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA.

citation:
  Sountoulidis, Alexandros et al. “A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.” Nature cell biology vol. 25,2 (2023): 351-365. doi:10.1038/s41556-022-01064-x


dataset_id: STDS0000175
species: Homo sapiens
tissues: Lung
development_stages: 7 weeks;11 weeks;10 weeks;9 weeks;8 weeks;12 weeks;6 weeks;8.5 weeks;13.5 weeks
technologies: 10x Visium
disease: Lung development
submission_date: 2022-10-17 00:00:00
last_modified: 2023-01-20 00:00:00
contributors: Czarnewski, Paulo;Sergio, Marco S;Alexandros, Sountoulidis;Paulo, Czarnewski;Christos, Samakovlis
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215897
platforms: Illumina NextSeq 500;Illumina NovaSeq 6000;NextSeq 2000
pmid: 36646791
has_paired: SCDS0000019
title:
  A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [ST]

summary:
  The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here, we report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programs, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell-types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

overall_design:
  One of the two lungs (preferentially the left), from each donor, was snap frozen in cryomatrix and further used for histological analyses. We cut 10-12μm-thick tissue sections with a cryostat (Leica CM3050S or analogue) and collected them onto poly-lysine coated slides (VWR Cat No. 631-0107)
  NOTE FROM SUBMITTER: raw reads from our cohort are considered sensate and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA.

citation:
  Sountoulidis, Alexandros et al. “A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.” Nature cell biology vol. 25,2 (2023): 351-365. doi:10.1038/s41556-022-01064-x


dataset_id: STDS0000178
title: Integration of whole transcriptome spatial profiling with protein markers
species: Mus musculus
tissues: Spleen;Breast
technologies: 10x Visium
disease: Nornal atlas
submission_date: 2022-03-10 00:00:00
last_modified: 2023-01-18 00:00:00
contributors: Niu, Xiang;Ben-Chetrit, Nir;Swett, Ariel;Stoeckius, Marlon;Landau, Dan A
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198353
platforms: Illumina NextSeq 500;Illumina NovaSeq 6000
pmid: 36593397
summary:
  Spatial transcriptomics and proteomics provide complementary information that independently transformed our understanding of complex biological processes. However, experimental integrations of these modalities are limited. To overcome this, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for high-throughput simultaneous integration of spatial transcriptomics and protein profiling. Compared to unimodal measurements, SPOTS substantially improves signal resolution and cell clustering and enhances the discovery power in differential gene expression analysis across tissue regions.

overall_design:
  Multimodal spatial profiling of whole transcriptomes and extracellular proteins in mouse spleen and breast cancer.

citation:
  Ben-Chetrit, Nir et al. “Integration of whole transcriptome spatial profiling with protein markers.” Nature biotechnology vol. 41,6 (2023): 788-793. doi:10.1038/s41587-022-01536-3


dataset_id: STDS0000171
species: Mus musculus
tissues: Legs
organ_parts: Hindpaw
development_stages: 10-12 weeks
technologies: 10x Visium
disease: Fibrotic tendon healing
submission_date: 2022-10-20 00:00:00
last_modified: 2023-01-06 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216214
platforms: NextSeq 550
pmid: 36417854
title:
  Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function

summary:
  Spatial transcriptomic analysis of murine FDL tendons following acute injury and repair to evaluate spatiotemporal programming of tendon healing

overall_design:
  Hindpaws from Scx-Ai9 mice (Scx-lin+ cells labeled with tdTomato fluorescence prior to surgery) were collected at D0, 14, 21, and 28 post-injury (in duplicate) for ST analysis of healing tendons using the 10X Visium platform

contributors:
  Ackerman, Jessica;Best, Katherine;Muscat, Samantha;Nichols, Anne;Pritchett, Elizabeth;Wu, Chia-Lung;Loiselle, Alayna

citation:
  Ackerman, Jessica E et al. “Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function.” Cell reports vol. 41,8 (2022): 111706. doi:10.1016/j.celrep.2022.111706


dataset_id: STDS0000205
title: Spatial transcriptomics landscape of non-communicable inflammatory skin diseases
species: Homo sapiens
tissues: Skin
technologies: 10x Visium
submission_date: 2022-06-17 00:00:00
last_modified: 2023-01-02 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206391
platforms: Illumina NovaSeq 6000
pmid: 36513651
disease:
  Psoriasis | Atopic dermatitis | Lichen planus | Pityriasis rubra pilaris / Psoriasis | Psoriasis, Lichen planus 

summary:
  We investigated the landscape of non-communicable inflammatory skin diseases by spatial transcriptomics resulting in a large repository of spatially defined human cutaneous transcriptomes of 31 patients.

overall_design:
  Dataset containing 90 spatial transcriptomic sequencing samples of skin biopsies taken from 31 patients diagnosed with psoriasis, atopic dermatitis or lichen planus, including duplicates of 31 lesional and 14 matched non-lesional samples. Samples  21L008958-21L008973 contain 2-3 specimen on a capture area from different patients and diseases.

contributors:
  Hillig, Christina;Schaebitz, Alexander;Mubarak, Menatullah;Jargosch, Manja;Farnoud, Ali;Scala, E.;Kurzen, Nils;Pilz, A.C.;Bhalla, N.;Thomas, J.;Stahle, M.;Biedermann, T.;Schmidt-Weber, C.B.;Theis, Fabian;Walzthoeni, Thomas;Garzorz-Stark, Natalie;Eyerich, Kilian;Menden, Michael;Eyerich, Stefanie

citation:
  Schäbitz, A et al. “Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases.” Nature communications vol. 13,1 7729. 13 Dec. 2022, doi:10.1038/s41467-022-35319-w


dataset_id: STDS0000188
species: Homo sapiens
tissues: Brain
organ_parts: Postmortem brain
technologies: 10x Visium
disease: Alzheimer disease
submission_date: 2022-12-07 00:00:00
last_modified: 2022-12-27 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220442
platforms: Illumina NovaSeq 6000
pmid: 36544231
title:
  Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease

summary:
  Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10x Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identify unique marker genes for cortical layers and the white matter, and layer-specific differentially expressed genes (DEGs) in human AD compared to CT. Deconvolution of the Visium spots showcases the significant difference in particular cell types among cortical layers and the white matter. Gene co-expression analyses reveal eight gene modules, four of which have significantly altered co-expression patterns in the presence of AD pathology. The co-expression patterns of hub genes and enriched pathways in the presence of AD pathology indicate an important role of cell-cell-communications among microglia, oligodendrocytes, astrocytes, and neurons, which may contribute to the cellular and regional vulnerability in early AD. Using single-molecule fluorescent in situ hybridization, we validated the cell-type-specific expression of three novel DEGs (e.g., KIF5A, PAQR6, and SLC1A3) and eleven previously reported DEGs associated with AD pathology (i.e., amyloid beta plaques and intraneuronal neurofibrillary tangles or neuropil threads) at the single cell level. Our results may contribute to the understanding of the complex architecture and neuronal and glial response to AD pathology of this vulnerable brain region.

overall_design:
  Human MTG was cryosectioned at 10 µm and mounted on the Visium GE slide for Visium profiling. Spatial resovled transcriptomic (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following 10x Visium user guide (CG000239 Rev A).

contributors:
  Wang, Cankun;Chen, Shuo;Chang, Yuzhou;Li, Liangping;Acosta, Diana;Li, Yang;Guo, Qi;Turkes, Emir;Morrison, Cody;Julian, Dominic;Hester, Mark E;Scharre, Douglas W;Santiskulvong, Chintda;Song, Xue Y;Plummer, Jasmine T;Serrano, Geidy E;Beach, Thomas G;Duff, Karen E;Ma, Qin;Fu, Hongjun

citation:
  Chen, Shuo et al. “Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer's disease.” Acta neuropathologica communications vol. 10,1 188. 21 Dec. 2022, doi:10.1186/s40478-022-01494-6


dataset_id: STDS0000153
species: Homo sapiens;Mus musculus
tissues: Overian
technologies: 10x Visium
disease: Overian cancer
submission_date: 2022-05-23 00:00:00
last_modified: 2022-12-11 00:00:00
contributors: Barkley, Dalia;Yanai, Itai
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203612
pmid: 35931863
has_paired: STDS0000153
title:
  Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

summary:
  Transcriptional heterogeneity among malignant cells of a tumor has been studied in individual cancer types and shown to be organized into cancer cell states; however, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of gene modules whose expression defines recurrent cancer cell states including ‘stress’, ‘interferon response’, ‘epithelial-mesenchymal transition’, ‘metal response’, ‘basal’ and ‘ciliated’. Spatial transcriptomic analysis linked the interferon response in cancer cells to T cells and macrophages in the tumor microenvironment. Using mouse models, we further found that induction of the interferon response module varies by tumor location and is diminished upon elimination of lymphocytes. Our work provides a framework for studying how cancer cell states interact with the tumor microenvironment to form organized systems capable of immune evasion, drug resistance, and metastasis.

overall_design:
  Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

citation:
  Barkley, Dalia et al. “Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment.” Nature genetics vol. 54,8 (2022): 1192-1201. doi:10.1038/s41588-022-01141-9

platforms:
  Illumina NextSeq 500 (Homo sapiens);Illumina NextSeq 500 (Mus musculus);Illumina NextSeq 500 (Homo sapiens; Mus musculus)


dataset_id: STDS0000181
species: Mus musculus
tissues: Brain
organ_parts: Coronal brain section
technologies: 10x Visium
disease: Alzheimer disease
submission_date: 2022-05-20 00:00:00
last_modified: 2022-12-09 00:00:00
contributors: Hasel, Philip;Liddelow, Shane A;Castranio, Emilie L;Ehrlich, Michelle E
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203424
platforms: Illumina NovaSeq 6000
pmid: 36448627
title:
  INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease

summary:
  Spatial Transcriptomics (Visium) of 12 coronal brain sections from 6 months old female Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice and treated with either cornoil or tamoxifen (75 mg/kg) at 3 months of age for 5 consecutive days

overall_design:
  Spatial Transcriptomics of Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice to study the transcriptomics, brain-region resolved effect of removing Inpp5d from microglia in an animal model of Alzheimer's disease

citation:
  Castranio, Emilie L et al. “Microglial INPP5D limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer's disease.” Alzheimer's & dementia : the journal of the Alzheimer's Association vol. 19,6 (2023): 2239-2252. doi:10.1002/alz.12821


dataset_id: STDS0000157
title: clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ
species: Homo sapiens
cell_types: melanoma cells;cell line:WM989 A6-G3
technologies: ClampFISH
disease: Melanoma
submission_date: 2022-08-17 00:00:00
last_modified: 2022-12-01 00:00:00
contributors: Goyal, Yogesh;Dardani, Ian;Raj, Arjun
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211491
platforms: NextSeq 550 (Homo sapiens)
pmid: 36280724
summary:
  We developed an amplified single-molecule RNA FISH method called clampFISH 2.0. To validate its performance, we used clampFISH 2.0 on two cell lines, WM989 A6-G3 cells and WM989 A6-G3 cells grown in vemurafenib, and across 10 genes, compared clampFISH 2.0 spot counts to the FPKM values from bulk RNA sequencing.

overall_design:
  Resistant colonies were isolated from a plate of WM989 A6-G3 cells which were treated with 1µM vemurafenib. Bulk RNA sequencing was performed as described in Goyal et al. 2021 (https://doi.org/10.1101/2021.12.08.471833) for each resistant colony as well as drug-naive WM989 A6-G3 cells. For this analysis, a single resistant colony was included for comparison to the drug-naive WM989 A6-G3 cells. Briefly, we conducted standard bulk paired-end (37:8:8:38) RNA sequencing using RNeasy Micro (Qiagen, 74004) for RNA extraction, NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB, E7600S), and an Illumina NextSeq 550 75 cycle high-output kit (Illumina, 20024906), as previously described (Mellis et al. 2021; Shaffer et al. 2017). Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. We aligned RNA-seq reads to the human genome (hg19) with STAR v2.5.2a and counted uniquely mapping reads with HTSeq v0.6.1 (Dobin et al. 2013; Mellis et al. 2021; Shaffer et al. 2017) and outputs count matrix. The counts matrix was used to obtain tpm and other normalized values for each gene using scripts provided at: https://github.com/arjunrajlaboratory/RajLabSeqTools/tree/master/LocalComputerScripts

citation:
  Dardani, Ian et al. “ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ.” Nature methods vol. 19,11 (2022): 1403-1410. doi:10.1038/s41592-022-01653-6


dataset_id: STDS0000186
title: Assessment of Spatial Genomics for Oncology Discovery
species: Rattus norvegicus;Homo sapiens;Mus musculus
tissues: Colon
organ_parts: Colon;Pancreatic cancer;B16F10 syngeneic tumor;MC38 syngeneic tumor
technologies: 10x Visium
disease: Cancer
overall_design: Anna, Lyubetskaya
submission_date: 2022-08-23 00:00:00
last_modified: 2022-11-29 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211895
platforms: Illumina NovaSeq 6000;Illumina NovaSeq 6000;Illumina NovaSeq 6000
pmid: 36452860
summary:
  Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for Oncology Discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis that provide a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.

contributors:
  Lyubetskaya, Anna;Rabe, Brian;Fisher, Andrew;Lewin, Anne;Neuhaus, Isaac;Brett, Connie;Brett, Todd;Pereira, Ethel;Golhar, Ryan;Kebede, Sami;Font-Tello, Alba;Mosure, Kathy;Van Wittenberghe, Nicholas;Mavrakis, Konstantinos;MacIsaac, Kenzie;Chen, Benjamin;Drokhlyansky, Eugene

citation:
  Lyubetskaya, Anna et al. “Assessment of spatial transcriptomics for oncology discovery.” Cell reports methods vol. 2,11 100340. 15 Nov. 2022, doi:10.1016/j.crmeth.2022.100340


dataset_id: STDS0000143
species: Mus musculus
tissues: Neuron
technologies: 10x Visium;scRNA
disease: Neuron regeneration
submission_date: 2021-05-11 00:00:00
last_modified: 2022-11-29 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174265
pmid: 36170369
title:
  Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.

cell_types:
  celltype:Stage 2;celltype:Baseline;celltype:Glia;celltype:primary neuron;celltype:Stage 1;celltype:microglia

summary:
  DNA double strand breaks (DSBs) are linked to neurodegeneration and senescence. However, it is not clear how DSB-bearing neurons influence neuroinflammation associated with neurodegeneration. Here, we characterize DSB-bearing neurons from the CK-p25 mouse model of neurodegeneration using single-nucleus, bulk, and spatial transcriptomic techniques. DSB-bearing neurons enter a late-stage DNA damage response marked by NFκB-activated senescent and antiviral immune pathways. In humans, Alzheimer’s disease pathology is significantly associated with immune activation in excitatory neurons. Spatial transcriptomics reveal that regions of CK-p25 brain tissue dense with DSB-bearing neurons harbor signatures of inflammatory microglia, which is ameliorated by NFκB knock-down in neurons. Inhibition of NFκB in DSB-bearing neurons also reduces microglia activation in organotypic mouse brain slice culture. In conclusion, DSBs activate immune pathways in neurons, which in turn adopt a senescence-associated secretory phenotype to elicit microglia activation. These findings highlight a novel role for neurons in the mechanism of disease-associated neuroinflammation.

overall_design:
  We used the CK-p25 mouse model of neurodegeneration to study the role of DSB-bearing neurons in neurodegeneration. Two male CK-p25 mice and two male CK mice were used for bulk RNA-sequencing. Stage 1, Stage 2, Baseline neurons, and Glia (so termed by NeuN and gH2AX imunoreactivity) were sorted from each mouse using FANS, then sequenced. For single-nucleus RNA-seq, Stage 1, Stage 2, Baseline neurons, and Glia were sorted and sequenced from three CK-p25 animals and three CK control littermates 1-week and 2-weeks after p25 induction. A total of 1,357 single nucleus libraries were prepared using SMARTseq2 chemistry. Three biological replicates each were used for bulk RNA-seq of etoposide-treated primary neurons (50um, 6hours), and dmso-control primary neurons. Three biological replicates each were used for bulk RNA-seq of FAN-sorted microglia nuclei from CK-p25 p65kd, CK-p25 Scramble, and CK Control PBS mice. Microglia nuclei were sorted based on PU.1 immunoreactivity.

contributors:
  Tsai, Li-Huei;Welch, Gwyneth M;Su, Qiao;Pfenning, Andreas R;Boix, Carles A;Kellis, Manolis;Schmauch, Eloi

citation:
  Welch, Gwyneth M et al. “Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.” Science advances vol. 8,39 (2022): eabo4662. doi:10.1126/sciadv.abo4662

platforms:
  Illumina MiSeq (Mus musculus);Illumina NextSeq 500 (Mus musculus);Illumina NovaSeq 6000 (Mus musculus)


dataset_id: STDS0000203
title: The neurons that restore walking after paralysis [snRNA-seq]
species: Mus musculus
tissues: Spinal cord
technologies: 10x Visium
disease: Paralysis
submission_date: 2021-09-17 00:00:00
last_modified: 2022-11-18 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184370
platforms: Illumina HiSeq 2500
pmid: 36352232
has_paired: STDS0000195
summary:
  Here, we show that epidural electrical stimulation (EES) of the lumbar spinal cord applied during neurorehabilitation (EESREHAB) restored walking in nine people with chronic spinal cord injury (SCI). This recovery involved a reduction of the metabolic activity in the lumbar spinal cord during walking. We hypothesized that this unexpected reduction reflects activity-dependent selection of specific neuronal subpopulations that become essential to walk after SCI. To identify these putative neurons, we modelled the technological and therapeutic features underlying EESREHAB in mice. We applied single-nucleus RNA sequencing and spatial transcriptomics to the spinal cord of these mice to chart a spatially-resolved molecular atlas of recovery from paralysis. We then employed cell type and spatial prioritization to uncover the neurons involved in the recovery of walking. A single population of excitatory interneurons nested within intermediate laminae emerged. Although these neurons were not necessary to walk before SCI, we demonstrate that they are essential to regain walking following SCI. In turn, augmenting their activity instantly phenocopied the recovery of walking enabled by EESREHAB. We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after SCI. Moreover, our methodology establishes a framework to identify the neurons producing complex behaviours using molecular cartography.

overall_design:
  We used single-nucleus RNA sequencing (snRNA-seq) to profile the lumbar spinal cord of mice. We devised a progression of eight experimental conditions that captured the key therapeutic features of EESREHAB. We obtained high-quality transcriptomes from 82,093 nuclei that were evenly represented across 24 mice from all eight conditions.

  Mice were divided in three experimental groups: uninjured, SCI (no neurorehabilitation), and EESREHAB. At the end of the experimental period, mice were terminated to harvest fresh tissues or perfused and dissected. Half of the groups of mice underwent a terminal experimental condition immediately before being terminated, which is denoted by     final_condition. If more than one component was integrated in the terminal experimental condition, the additional component is denoted by  ::. Group 1 (uninjured) consisted of uninjured mice that did not perform a terminal behavioral task. Mice in Group 2 (SCI) received a contusion SCI and did not perform a terminal behavioral task. Mice in Group 3 (EESREHAB) received a contusion SCI and followed EESREHAB  for four weeks, but did not perform a terminal behavioral task.  Mice in Group 4 (SCI   EES::walking) received a contusion SCI and walked with EESON  for 30 minutes immediately before being terminated. Mice in Group 5 (EESREHAB   EES::walking) received a contusion SCI and followed EESREHAB  for four weeks, and walked with EESON  for 30 minutes immediately before being terminated. Mice in Group 6 (EESREHAB   EES) received a contusion SCI and and followed EESREHAB  for four weeks, and were stimulated for 30 minutes with EES just below motor threshold immediately before being terminated. Mice in Group 7 (EESREHAB   EES::cortex) received a contusion SCI and followed EESREHAB  for four weeks, and walked with optogenetic stimulation of the motor cortex for 30 minutes immediately before being terminated. Mice in Group 8 (EESREHAB   EES::cortex::walking) received a contusion SCI and followed EESREHAB  for four weeks, and walked with EESON  and optogenetic stimulation of the motor cortex for 30 minutes immediately before being terminated.

contributors:
  Squair, Jordan W;Kathe, Claudia;Skinnider, Michael A;Hutson, Thomas;Regazzi, Nicola;Gautier, Matthieu;Demesmaeker, Robin;Komi, Salif;Ceto, Steven;James, Nicholas D;Cho, Newton;Baud, Laetitia;Galan, Katia;Matson, Kaya J;Rowald, Andreas;Kim, Kyungjin;Wang, Ruijia;Prior, John O;Asboth, Leonie;Barraud, Quentin;Lacour, Stephanie P;Levine, Ariel J;Wagner, Fabien;Bloch, Jocelyne;Courtine, Grégoire

citation:
  Kathe, Claudia et al. “The neurons that restore walking after paralysis.” Nature vol. 611,7936 (2022): 540-547. doi:10.1038/s41586-022-05385-7


dataset_id: STDS0000182
title: Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.
species: Mus musculus
tissues: Lacrimal Gland
development_stages: 4 months
sex: Male
technologies: 10x Visium
disease: Gland repair
submission_date: 2022-08-02 00:00:00
last_modified: 2022-11-17 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210380
platforms: NextSeq 2000
pmid: 36341342
summary:
  To identify the transcriptomic alterations within the different cellular compartments of the lacrimal gland during chronic inflammation, we analyzed the lacrimal glands of NOD.B10.H2b vs BALB/cJ with 10X Visium technology

overall_design:
  We sequenced RNA from lacrimal glands cryosections (10μm) of BALB/cJ (control) and NOD.H2b (disease) mice aged of 4 months in duplicates.

contributors:
  Makarenkova, Helen;Mauduit, Olivier;Delcroix, Vanessa;Umazume, Takeshi;de Paiva, Cintia S;Dartt, Darlene A;Makarenkova, Helen P

citation:
  Mauduit, Olivier et al. “Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation.” Frontiers in immunology vol. 13 1011125. 17 Oct. 2022, doi:10.3389/fimmu.2022.1011125


dataset_id: STDS0000154
species: Homo sapiens
tissues: Colon
organ_parts: Skin irAE
technologies: 10x Visium
disease: Dermatitis and Colitis
overall_design: spatial transcriptomics: skin irAE vs. Psoriasis, colon irAE vs. healthy colon
submission_date: 2022-07-29 00:00:00
last_modified: 2022-11-07 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210037
platforms: Illumina NovaSeq 6000 (Homo sapiens)
pmid: 35977003
title:
  Checkpoint blockade-induced dermatitis and colitis are dominated by tissue resident memory T cells and  Th1/Tc1 cytokines

summary:
  Immune checkpoint blockade (ICB) is therapeutically successful in multiple cancer types. However, immune-related adverse events (irAE) frequently occur and can sometimes be life-threatening.
  It is critical to understand the immunologic mechanisms of irAEs with the goal of finding novel treatment targets. Therefore, we studied tissues from irAE dermatitis cases using multiparameter immunofluorescence (IF), spatial transcriptomics,
  and RNA in situ hybridization. Skin psoriasis cases were studied as a comparison, as a known Th17-driven disease, and colitis was investigated as a comparison. IF analysis revealed that CD4+ and CD8+ tissue resident memory T (TRM) cells
  were preferentially expanded in the inflamed portion of skin in cutaneous irAEs compared to healthy skin controls. Spatial transcriptomics allowed focusing attention on areas containing TRM cells to discern their functional phenotype,
  and revealed expression of Th1-associated genes in irAE, compared to Th17-asociated genes in psoriasis. Expression of a range of inhibitory checkpoint molecules was observed, including PD-1, CTLA-4, LAG-3, and TIGIT.
  RNA in situ hybridization (RISH) technology combined with IF confirmed expression of IFN-γ, CXCL9, CXCL10, and TNF-α in additional irAE dermatitis cases and allowed us to identify production of IFN-γ within TRM cells specifically. The Th1-skewed phenotype was confirmed in irAE colitis cases compared to healthy colon.

contributors:
  Reschke, Robin;Gajewski, Thomas F;Yu, Jovian;Rouhani, Sherin J;Olson, Daniel J;Zha, Yuanyuan;Shapiro, Jason W

citation:
  Reschke, Robin et al. “Checkpoint Blockade-Induced Dermatitis and Colitis Are Dominated by Tissue-Resident Memory T Cells and Th1/Tc1 Cytokines.” Cancer immunology research vol. 10,10 (2022): 1167-1174. doi:10.1158/2326-6066.CIR-22-0362


dataset_id: STDS0000159
title: The Deciphering of Mouse Uterine Microenvironment during Early Pregnancy
species: Mus musculus
tissues: Uterus
organ_parts: Embryo implantation site
development_stages: E7.5
technologies: 10x Visium;scRNA
disease: Early Pregnancy
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2021-07-30 00:00:00
last_modified: 2022-10-29 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181170
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 35357464
citation:
  Li, Rong et al. “Spatial transcriptomic profiles of mouse uterine microenvironments at pregnancy day 7.5†.” Biology of reproduction vol. 107,2 (2022): 529-545. doi:10.1093/biolre/ioac061


dataset_id: STDS0000158
title: Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage
species: Homo sapiens
tissues: Heart
organ_parts: Myocardium
technologies: GeoMx DSP
disease: COVID-19
submission_date: 2022-08-26 00:00:00
last_modified: 2022-10-28 00:00:00
contributors: Kulasinghe, A K;Tan, C W
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212119
platforms: Illumina NovaSeq 6000 (Homo sapiens);Illumina NovaSeq 6000 (blank sample)
pmid: 36107637
summary:
  In this study, we investigated the landscape of cardiac tissues collected at rapid autopsy from 7 SARS-CoV-2, 2 pH1N1, and 6 control patients using targeted spatial transcriptomics approaches. The main outcomes for the study were to profile rapid autopsy samples collected from the COVID-19, pH1N1 and normal, non-viral deaths to determine transcriptional changes between the different cohorts. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by g-H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of Interferon-stimulated genes (ISGs), in particular interferon and complement pathways, when compared with COVID-19 patients.

overall_design:
  In this dataset, we capture GeoMx DSP RNA profiles of myocardial tissue from SARS-CoV2 infected patients aswell as pH1N1 and control specimens

citation:
  Kulasinghe, Arutha et al. “Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage.” Immunology vol. 168,3 (2023): 403-419. doi:10.1111/imm.13577


dataset_id: STDS0000149
title: Spatiotemporal transcriptomes of orchid flowers
species: Phalaenopsis aphrodite
tissues: Flower
organ_parts: Sagittal section
development_stages: 8 days after budding
technologies: 10x Visium
disease: Plants
overall_design: Phalaenopsis Big Chili flowers at early developing stages sequenced on 10X Visium platform
submission_date: 2022-03-08 00:00:00
last_modified: 2022-10-24 00:00:00
contributors: Liu, Chang;Leng, Jing;Li, Yonglong;Ge, Tingting;Li, Jinglong;Chen, Yamao;Guo, Chunce;Qi, Ji
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198128
platforms: Illumina NovaSeq 6000 (Phalaenopsis aphrodite)
pmid: 36095130
summary:
  We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.

citation:
  Liu, Chang et al. “A spatiotemporal atlas of organogenesis in the development of orchid flowers.” Nucleic acids research vol. 50,17 (2022): 9724-9737. doi:10.1093/nar/gkac773


dataset_id: STDS0000165
species: Oryctolagus cuniculus
tissues: Muscle
technologies: 10x Visium
disease: Rotator cuff tear
submission_date: 2022-08-08 00:00:00
last_modified: 2022-10-14 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210773
platforms: Illumina NovaSeq 6000 (Oryctolagus cuniculus)
pmid: 36195913
title:
  Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear

summary:
  Conditions affecting skeletal muscle, such as chronic rotator cuff tears, low back pain, dystrophies, and many others often share changes in muscle phenotype: intramuscular adipose and fibrotic tissue increase while contractile tissue is lost. The underlying changes in cell populations and cell ratios observed with these phenotypic changes complicate the interpretation of tissue-level transcriptional data. Novel single cell transcriptomics has limited capacity to address this problem because muscle fibers are too long to be engulfed in single cell droplets and single nuclei transcriptomics are complicated by muscle fibers’ multinucleation. Therefore, the goal of this project was to evaluate the potential and challenges of a spatial transcriptomics technology to add dimensionality to transcriptional data in an attempt to better understand regional cellular activity in heterogeneous skeletal muscle tissue.

overall_design:
  Fresh and 6 years old snapfrozen healthy and tenotomized rabbit supraspinatus muscle sections were mounted on 10x Visium slides

contributors:
  Ruoss, Severin;Esparza, Mary C;Vasquez-Bolanos, Laura S;Nasamran, Chanond A;Fisch, Kathleen M;Engler, Adam J;Ward, Samuel R

citation:
  Ruoss, Severin et al. “Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear.” Journal of orthopaedic surgery and research vol. 17,1 440. 4 Oct. 2022, doi:10.1186/s13018-022-03326-8


dataset_id: STDS0000164
title: Spatial gene expression-based, non-small cell lung carcinoma patients with paired brain metastases
species: Homo sapiens
tissues: Lung
technologies: GeoMx DSP
disease: Non-small cell lung cancer
submission_date: 2022-04-10 00:00:00
last_modified: 2022-10-12 00:00:00
contributors: Abdo, Rober
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200563
platforms: NextSeq 550 (Homo sapiens)
pmid: 36216799
cell_types:
  Metastatic lung cancer in a lymph node;tumor immune microenviroment in the metastatic brain;tumor immune microenviroment in the primary lung cancer;Metastatic lung cancer in the brain;primary lung cancer;non-tumor brain;tumor brain microenviroment in metastatic brain

summary:
  Spatial RNA-seq were successfully constructed through expression profiling of a total of 18,694 genes in non-small cell lung cancer (NSCLC) cases with paired brain metastases.

overall_design:
  In the study presented here, 35 cases from a well-defined cohort of 44 NSCLC cases with paired brain metastases was used to acquire expression profiles of a total of 18,694 unique genes.

citation:
  Zhang, Qi et al. “The spatial transcriptomic landscape of non-small cell lung cancer brain metastasis.” Nature communications vol. 13,1 5983. 10 Oct. 2022, doi:10.1038/s41467-022-33365-y


dataset_id: STDS0000160
title: A cellular hierarchy in melanoma uncouples growth and metastasis
species: Homo sapiens;Mus musculus
tissues: Skin
organ_parts: Tail skin
cell_types: cell line:MM047
technologies: 10x Visium;scRNA;Stereo-Seq
disease: Melanoma
overall_design: scRNA-Seq and bulk RNA-Seq
submission_date: 2022-07-06 00:00:00
last_modified: 2022-10-07 00:00:00
contributors: Rambow, Florian;Karras, Panagiotis;Pozniak, Joanna
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207592
platforms: Illumina NovaSeq 6000 (Homo sapiens);DNBSEQ-G400 (Mus musculus);Illumina NovaSeq 6000 (Mus)
pmid: 36131018
summary:
  Although melanoma is notorious for its high degree of heterogeneity and plasticity, the origin and magnitude of cell state diversity remains poorly understood. Equally, it is not known whether melanoma growth and metastatic dissemination are supported by overlapping or distinct melanoma subpopulations. By combining mouse genetics, unbiased lineage tracing and quantitative modelling, single-cell and spatial transcriptomics, we provide evidence of a hierarchical model of tumour growth that mirrors the cellular and molecular logic underlying embryonic neural crest cell fate specification and differentiation. Our findings indicate that tumorigenic competence is associated with a spatially localized perivascular niche environment, a phenotype acquired through a NOTCH3-dependent intercellular communication pathway established by endothelial cells. Consistent with a model in which only a fraction of melanoma cells is fated to fuel growth, temporal single-cell tracing of a population of melanoma cells harbouring a mesenchymal-like state revealed that these cells do not contribute to primary tumour growth but, instead, constitutes a pool of metastatic-initiating cells that can switch cell identity while disseminating to secondary organs. Our data provide a spatially and temporally resolved map of the diversity and trajectories of cancer cell states within the evolving melanoma ecosystem and suggest that the ability to support growth and metastasis are limited to distinct pools of melanoma cells. The observation that these phenotypic competencies can be dynamically acquired upon exposure to specific niche signals warrant the development of therapeutic strategies that interfere with the cancer cell reprogramming activity of such microenvironmental cues.

citation:
  Karras, Panagiotis et al. “A cellular hierarchy in melanoma uncouples growth and metastasis.” Nature vol. 610,7930 (2022): 190-198. doi:10.1038/s41586-022-05242-7


dataset_id: STDS0000152
title: Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma
species: Homo sapiens
tissues: Lymph
organ_parts: lymphoma
technologies: 10x Visium
disease: CNS lymphoma
submission_date: 2022-05-22 00:00:00
last_modified: 2022-09-25 00:00:00
contributors: Heming, Michael;Lu, I-Na;Grauer, Oliver;Meyer zu Hörste G
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203552
platforms: Illumina NovaSeq 6000 (Homo sapiens);NextSeq 2000 (Homo sapiens)
pmid: 36153593
has_paired: STDS0000152
summary:
  Single-cell transcriptomic atlas of leukocytes of biopsy fluid (n = 2), blood (n = 2) and CSF (n = 1), and spatial transcriptomics of biopsy tissue (n = 4) from primary CNS B cell lymphoma patients.

overall_design:
  Single-cell RNA and BCR sequencing of paired biopsy fluid and blood and spatial transcriptomics in primary CNS lymphoma.

citation:
  Heming, Michael et al. “Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma.” Genome medicine vol. 14,1 109. 24 Sep. 2022, doi:10.1186/s13073-022-01110-1


dataset_id: STDS0000155
title: Spatial transcriptomics of TSC angiomyolipoma
species: Homo sapiens
tissues: Kidney
organ_parts: Angiomyolipoma (AML)
technologies: GeoMx DSP
disease: Angiomyolipoma
submission_date: 2022-08-08 00:00:00
last_modified: 2022-09-15 00:00:00
contributors: Tang, Yan
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210755
platforms: Illumina NovaSeq 6000 (Homo sapiens)
pmid: 36028490
summary:
  We performed spatial transcriptomics on one IS-dominant tumor and on SLS-dominant tumor. Our goal was to determin different immune infiltration in these two subtypes.

overall_design:
  NanoString Digital Spatial Profiling (DSP) with Whole Transcriptome Atlas (WTA) was performed on one IS-dominant and one SLS-dominant tumor, with each tumor profiled for 12 ROIs.

citation:
  Tang, Yan et al. “Midkine expression by stem-like tumor cells drives persistence to mTOR inhibition and an immune-suppressive microenvironment.” Nature communications vol. 13,1 5018. 26 Aug. 2022, doi:10.1038/s41467-022-32673-7


dataset_id: STDS0000147
species: Mus musculus
tissues: Lung
development_stages: 6-8 weeks
technologies: 10x Visium;scATAC;scRNA
disease: Normal atlas
submission_date: 2021-12-06 00:00:00
last_modified: 2022-09-12 00:00:00
contributors: Xu, Zhongli;Chen, Wei;Chen, Kong
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190225
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 36039299
title:
  Integrative Analysis of Spatial Transcriptome with Single-cell Transcriptome and Single-cell Epigenome in Mouse Lungs after Immunization

summary:
  Immunological memory is key to productive adaptive immunity. An unbiased, high through-put gene expression profiling of tissue-resident memory T cells residing in various anatomical location within the lung is fundamental to understand lung immunity but still lacking. In this study, using a well-established model on Klebsiella pneumoniae, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after Immunization using the 10x Genomics Chromium and Visium platform. We employed several deconvolution algorithms and established an optimized deconvolution pipeline to accurately decipher specific cell-type composition by location. We identified and located 12 major cell types by scRNA-seq and spatial transcriptomic analysis.  Integrating scATAC-seq data from the same cells processed in parallel with scRNA-seq, we found epigenomic profiles provide more robust cell type identification, especially for lineage-specific T helper cells. When combining all three data modalities, we observed a dynamic change in the location of T helper cells as well as their corresponding chemokines for chemotaxis. Furthermore, cell-cell communication analysis of spatial transcriptome provided evidence of lineage-specific T helper cells receiving designated cytokine signaling. In summary, our first-in-class study demonstrated the power of multi-omics analysis to uncover intrinsic spatial- and cell-type-dependent molecular mechanisms of lung immunity. Our data provides a rich research resource of single cell multi-omics data as a reference for understanding spatial dynamics of lung immunization.

overall_design:
  In this study, we inoculated mice with heat-killed K. pneumoniae and assigned them into two groups, the immunized and the re-challenged group. The immunized group was inoculated twice on day 0 and day 7, whereas the re-challenged group was additionally inoculated on day 13. On day 14, both groups of mice were sacrificed for tissue harvesting. Slices A1 and A2 were sectioned from the fresh frozen lung of the immunized mouse, whereas slices A3 and A4 were from the re-challenged mouse. In a separate cohort, lung tissue from the re-challenged mouse were harvested and single-cell suspension was obtained after enzymatic digestion. The four lung slices were used for spatial transcriptomics, and the single-cell suspension from the re-challenged mouse were subjected to scRNA-seq and scATAC-seq analysis.

citation:
  Xu, Zhongli et al. “Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization.” iScience vol. 25,9 104900. 9 Aug. 2022, doi:10.1016/j.isci.2022.104900


dataset_id: STDS0000151
title: Resident Macrophage Subpopulations Occupy Distinct Microenvironments in the Kidney
species: Mus musculus
tissues: Kidney
organ_parts: Kidney-resident macrophages (KRMs)
technologies: 10x Visium;scRNA
disease: Quiescent/Uninjured
submission_date: 2022-04-04 00:00:00
last_modified: 2022-09-07 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200115
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 36066976
summary:
  The kidney contains a population of resident macrophages from birth that expands as it grows and forms a contiguous network throughout the tissue. Kidney resident macrophages (KRMs) are important in homeostasis and the response to acute kidney injury (AKI). While the kidney contains many microenvironments, it is unknown whether KRMs are a heterogeneous population differentiated by function and location. We combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, flow cytometry, and immunofluorescence imaging to localize, characterize, and validate KRM populations during quiescence and following 19 minutes of bilateral ischemic kidney injury. scRNAseq and spatial transcriptomics revealed seven distinct KRM subpopulations, which are organized into zones corresponding to regions of the nephron. Each subpopulation was identifiable by a unique transcriptomic signature suggesting distinct functions. Specific protein markers were identified for two clusters allowing analysis by flow cytometry or immunofluorescence imaging. Following injury, the original localization of each subpopulation is lost, either from changing locations or transcriptomic signatures. The original spatial distribution of KRMs is not fully restored for at least 28 days post-injury. The change in KRM localization confirms a long hypothesized dysregulation of the local immune system following acute injury and may explain the increased risk for chronic kidney disease.

overall_design:
  Single-cell RNA sequencing of kidneys leukocytes and spatial transcriptomics of whole kidneys obtained mice before and after bilateral ischemia reperfusion injury. There are five timepoints (quiescent/day 0, day 1, day 6, and day 28 with n=3 per timepoint for both single-cell and spatial transcriptomics

contributors:
  Cheung, Matthew D;Erman, Elise N;Moore, Kyle H;Lever, Jeremie M;Li, Zhang;LaFontaine, Jennifer R;Ghajar-Rahimi, Gelare;Liu, Shanrun;Yang, Zhengqin;Karim, Rafay;Li, Zhang;Yoder, Bradley K;Agarwal, Anupam;George, James F

citation:
  Cheung, Matthew D et al. “Resident macrophage subpopulations occupy distinct microenvironments in the kidney.” JCI insight vol. 7,20 e161078. 24 Oct. 2022, doi:10.1172/jci.insight.161078


dataset_id: STDS0000145
title: Geography and molecular anatomy of germ layers in the gastrulating primate embryo
species: Macaca fascicularis
tissues: Embryo
organ_parts: Gastrulation embryos
development_stages: E20
technologies: Geo-seq
disease: Normal atlas
submission_date: 2021-08-26 00:00:00
last_modified: 2022-09-06 00:00:00
contributors: Cui, Guizhong;Si, Wei;Jing, Naihe;Peng, Guangdun
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182838
platforms: Illumina NovaSeq 6000 (Macaca fascicularis)
pmid: 36044859
summary:
  During mammalian embryogenesis, temporal and spatial regulation of gene expression and cell signaling influences lineage specification, the patterning of tissue progenitors and the morphogenesis of embryo. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about early human and non-human primate gastrulation due to the limitation of technical and ethical. Here, we present a morphological and molecular approach that reveals the systematically morphological changes and comprehensive transcriptional landscape of cell types populating the non-human primate embryos during gastrulation.

overall_design:
  By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on Crab-eating macaque embryo sections at a high resolution of 5-50 cells per sample. We then constructed a comprehensive spatial transcriptome map in gastrulating embryos.

citation:
  Cui, Guizhong et al. “Spatial molecular anatomy of germ layers in the gastrulating cynomolgus monkey embryo.” Cell reports vol. 40,9 (2022): 111285. doi:10.1016/j.celrep.2022.111285


dataset_id: STDS0000167
species: Homo sapiens
tissues: Basal cell
organ_parts: Basal cell carcinoma
technologies: GeoMx DSP
disease: Basal cell carcinoma
submission_date: 2022-08-05 00:00:00
last_modified: 2022-08-29 00:00:00
contributors: Yerly L;Tissot S;Kuonen F
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210648
pmid: 35986012
title:
  Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma (Digital Spatial Profiling)

summary:
  To progress, tumors need to invade the surrounding tissues. However, the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insights for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas (BCCs), we define the cellular contributors of the invasive front. In the invasive niche, tumor cells harbor a collective migration phenotype, supported by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts (CAFs) with extracellular matrix-remodeling features, as required to support collective migration. Moreover, while tumor cells specifically express Activin A, we find Activin A-induced gene signature enrichment in adjacent CAFs subpopulations, further supporting their biological crosstalk. Altogether, our data identify the subpopulations and their transcriptional reprogramming contributing to the spatial organization of the BCC invasive niche. They also bring the proof-of-concept for integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop therapeutic targeting.

overall_design:
  Total 95 areas of interest from 12 basal cell carcinomas were sequenced using Digital Spatial Profiling (DSP) using GeoMX Nanostring, with the Cancer Transcriptome Altas (1812 genes)

citation:
  Yerly, Laura et al. “Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma.” Nature communications vol. 13,1 4897. 20 Aug. 2022, doi:10.1038/s41467-022-32670-w

platforms:
  Cancer Transcriptomic Atlas, Human, 1812 genes, Nanostring GeoMx Digital Spatial Profiling (DSP) Pla


dataset_id: STDS0000162
title: Spatial transcriptomics of the ageing ovary
species: Mus musculus
tissues: Ovarian
organ_parts: Follicles
development_stages: 3-4 months;15-16 months
technologies: 10x Visium
disease: Infertility
submission_date: 2021-11-05 00:00:00
last_modified: 2022-08-25 00:00:00
contributors: Russ, Jennifer E;Haywood, Mary E;Lane, Sydney C;Schoolcraft, William B;Katz-Jaffe, Mandy G
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188257
platforms: NextSeq 550 (Mus musculus)
pmid: 35996587
has_paired: SCDS0000010
summary:
  Ageing is a physiological process that manifests through progressive molecular, cellular, and systemic changes. Female reproductive potential gradually declines with age as oocyte quality and quantity decline. The purpose of this study was to better understand the spatiotemporal dynamics of the ovary.

overall_design:
  The Visium Spatial Gene Expression technology from 10x Genomics was used to evaluate expression in ovary sections from young (3-4 months) and aged (15-16 months) mice. RNA was captured and sequenced from 4 capture areas, each containing 2 ovary sections (one young, one aged) for a total of 4 young and 4 aged samples.

citation:
  Russ, Jennifer E et al. “Spatially resolved transcriptomic profiling of ovarian aging in mice.” iScience vol. 25,8 104819. 4 Aug. 2022, doi:10.1016/j.isci.2022.104819


dataset_id: STDS0000156
title: Temporal dynamics of macrophage heterogeneity after myocardial infarction
species: Mus musculus
tissues: Heart
cell_types: sorted CD45+ leukocytes
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-12-14 00:00:00
last_modified: 2022-08-24 00:00:00
contributors: Jung, Seung-Hyun;Chang, Kiyuk;Chung, Yeun-Jun
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163129
platforms: Illumina HiSeq 2500 (Mus musculus)
pmid: 35933399
summary:
  In this study, we attempted to identify the heterogeneity and temporal dynamics of leukocytes at single-cell level in mouse heart after inducing MI using the longitudinal single-cell RNA sequencing and spatial transcriptome sequencing.

overall_design:
  To obtain a comprehensive landscape of immune cell profiling after ischemic injury of heart, we performed single-cell RNA sequencing on flow cytometry sorted CD45+ leukocytes from infarcted area of the heart at 1, 3, 5, and 7 days after inducing MI in mice. CD45+ cells from the steady state (no MI) mice were also used for single-cell RNA sequencing as a control.

citation:
  Jung, Seung-Hyun et al. “Spatiotemporal dynamics of macrophage heterogeneity and a potential function of Trem2<sup>hi</sup> macrophages in infarcted hearts.” Nature communications vol. 13,1 4580. 6 Aug. 2022, doi:10.1038/s41467-022-32284-2


dataset_id: STDS0000148
title: Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]
species: Mus musculus
tissues: Neuron
organ_parts: Microglia
development_stages: 8-10 weeks
sex: male
technologies: 10x Visium;MERFISH
disease: Brain Cortex
overall_design: Examination of Mg states from different neuronal niches of the cerebral cortex.
submission_date: 2022-01-15 00:00:00
last_modified: 2022-08-17 00:00:00
contributors: Stogsdill, Jeffrey A;Kim, Kwanho;Binan, Loic;Farhi, Samouil L;Levin, Joshua Z;Arlotta, Paola
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193760
platforms: Microglia MERFISH
pmid: 35948630
summary:
  Microglia are the resident immune cells of the brain, and have critical roles in circuit development and plasticity. During embryonic and postnatal development, microglia exist in multiple transcriptional states. However, it is still poorly understood how these states are established, and whether they are influenced by their cellular environment. Here we show that in the juvenile neocortex, microglia exist in multiple states whose identity and laminar distribution is instructed by the neuronal class identity of local pyramidal neurons. Using single-cell RNA sequencing, we unveil molecular signatures of distinct microglia sub-states, and show that they can be divided into layer-restricted or broadly-distributed states. Strikingly, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures both the density and molecular state of local layer-restricted microglia to correspond to the new neuronal niche, thus identifying specific populations of microglia that are sensitive to pyramidal neuron subtypes. Ligand-receptor interactomes for individual neuronal subtype-microglia pairings uncovers two categories of neuron-to-microglia communication: one associated with neuronal class identity and one associated with microglial state. Our findings highlight the fundamental role that neuronal identity and neuronal niches play in locally controlling the transcriptional status of postnatal microglia.

citation:
  Stogsdill, Jeffrey A et al. “Pyramidal neuron subtype diversity governs microglia states in the neocortex.” Nature vol. 608,7924 (2022): 750-756. doi:10.1038/s41586-022-05056-7


dataset_id: STDS0000144
title: Spatial charting of single-cell transcriptomes in tissues
species: Homo sapiens
tissues: Breast
technologies: 10x Visium;scRNA
disease: Ductal carcinoma in situ
submission_date: 2021-07-31 00:00:00
last_modified: 2022-08-16 00:00:00
contributors: Wei, Runmin;He, Siyuan;Navin, Nicholas
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181254
platforms: Illumina NovaSeq 6000 (Homo sapiens)
pmid: 35314812
summary:
  We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization.

overall_design:
  We developed a computational method called CellTrek that combines single-cell RNA sequencing and spatial transcriptomics datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches.

citation:
  Wei, Runmin et al. “Spatial charting of single-cell transcriptomes in tissues.” Nature biotechnology vol. 40,8 (2022): 1190-1199. doi:10.1038/s41587-022-01233-1


dataset_id: STDS0000197
title: A spatiotemporal regulatory network for steroidogenesis of human fetal adrenal glands and gonads
species: Homo sapiens
tissues: Gland
organ_parts: Adrenal tissue;Gonad tissue
development_stages: 7 PCW;9 PCW;10 PCW;13 PCW;14 PCW
sex: F/M
technologies: 10x Visium
disease: Gland development
submission_date: 2021-02-26 00:00:00
last_modified: 2022-08-10 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167860
platforms: Illumina NovaSeq 6000
pmid: 36465633
summary:
  Human fetal adrenal glands are huge endocrine organ, produce prodigious quantities of dehydroepiandrosterone and its sulfate (DHEA/DHEAS), which is the most prominent precursor for steroid hormones, adrenal gonads dysfunction leads to states of virilization or effemination. However, for a long time the function of fetal adrenal in initial sex differentiation is unclear. Herein, we draw out a single-cell transcriptional landscape of human fetal adrenals and gonad from 6 to 14 gestational weeks (GW). We found that the adrenal glands begin to express CYP17A1 steroid-related enzyme much early than testis, subsequent testis steroid express pattern support de novo or halfway testosterone synthesis. Excepted steroidogenic cell, notably, the immune cells or neurocyte shows steroid metabolism or regulation ability, such as CD5L+ macrophage interacted with steroidogenic cell and SRD5A1+ AKR1C2+ chromaffin cells synthesis active testosterone DHT through backdoor pathway. Sex different were found at adrenal glands and gonad development: there is a small HSD3B2 peak occurs only in female adrenal glands around 10-12 GW within the time window of sex differentiation. SST expression levels or SST+ cells quantity in adrenal glands and gonads are different in two gender. Our research indicates that a sex different in spatial and temporal disparities steroidogenic regulatory networks in adrenal glands and gonads, facilitating further exploration of development and physiology of human adrenal glands.

overall_design:
  Adrenal and gonad samples from 6-14 GW human fetuses were used for single cell RNA sequencing by 10X Genomics

contributors:
  yifu, wang;Wang, Yifu;Guo, Bingqian;Guo, Yajie;Qi, Nana;Lv, Yufang;Ye, Yu;Huang, Yan;Long, Xinyang;Chen, Hongfei;Su, Cheng;Zhang, Liying;Zhang, Qingyun;Li, Minxi;Liao, Jingling;Yan, Yunkun;Mao, Xingning;Zeng, Yanyu;Jiang, Jinghang;Chen, Zhongyuan;Guo, Yi;Gao, Shuai;Cheng, Jiwen;Jiang, Yonghua;Mo, Zengnan

citation:
  Wang, Yifu et al. “A spatiotemporal steroidogenic regulatory network in human fetal adrenal glands and gonads.” Frontiers in endocrinology vol. 13 1036517. 17 Nov. 2022, doi:10.3389/fendo.2022.1036517


dataset_id: STDS0000146
title: Seq-Scope analysis of human acne
species: Homo sapiens
tissues: Skin
technologies: Seq-Scope
disease: Acne
summary: Skin samples were analyzed through Seq-Scope.
submission_date: 2021-10-26 00:00:00
last_modified: 2022-07-25 00:00:00
contributors: Hsu, Jer-En;Cho, Chun-Seok;Kim, Myungjin;Xi, Jingyue;Gudjonsson, Johann E;Lee, Jun Hee
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186601
platforms: Illumina HiSeq 2500 (synthetic construct);HiSeq X Ten (Homo sapiens)
pmid: 35867799
overall_design:
  A 6 mm punch skin biopsy was frozen in OCT medium and stored at -80°C until sectioning. The current study utilized Seq-Scope[HISEQ], which is similar to the previously described version of Seq-Scope [MISEQ] (PMID: 34115981), but utilized the HISEQ2500 flow cells for Seq-Scope array generation, instead of the MISEQ flow cells. All the procedures are extensively described in the former paper, and current study was performed almost identically; however, following things were different between the two studies: (1) To perform the 1st-Seq process, HISEQ2500 sequencing was performed with 100 pM of HDMI32-oligo library, and generated 1.1 million clusters/mm^2 fully sequenced pixel density (PF clusters). (2) HISEQ2500 tiles have a rectangular shape and are arranged to form a minimally interrupted large imaging area. Therefore, images from individual tiles were assembled to present a larger image that can be aligned with the hematoxylin and eosin histology results. (3) To accommodate the larger imaging area, volume of the solutions was proportionally increased during the experiment. (4) During the secondary strand synthesis, we used an updated Randomer sequence (5’-TCAGACGTGTGCTCTTCCGATCTNNNNNNNNB-3’). Compared to the original Randomer (5’-TCAGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’), the updated Randomer sequence does not anneal to the poly-A region, enabling more efficient transcriptome alignment. (5) To further substantiate our former results from scRNA-seq and spatial-seq, we focused on one acne sample, which presented an ideal spatial orientation that reveals the relationship between diverse inflammatory populations (including TREM2 macrophages) and hair follicle pathology. Other experi

citation:
  Do, Tran H et al. “TREM2 macrophages induced by human lipids drive inflammation in acne lesions.” Science immunology vol. 7,73 (2022): eabo2787. doi:10.1126/sciimmunol.abo2787


dataset_id: STDS0000166
title: Redefining electrical stimulation safety using spatial transcriptomics
species: Rattus norvegicus
tissues: Brain
organ_parts: Visual cortex
technologies: 10x Visium
disease: Brain cortex
overall_design: 10 micron tissue section from Long-evans rat visual cortex ~600 microns deep
submission_date: 2022-05-06 00:00:00
last_modified: 2022-07-01 00:00:00
contributors: Whitsitt, Quentin;Koo, Beomseo;Celik, Mahmut E;Evans, Blake;Purcell, Erin K;Weiland, James D
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202425
platforms: Illumina NovaSeq 6000 (Rattus norvegicus)
pmid: 35928007
summary:
  Current standards for safe delivery of electrical stimulation to the central nervous system are based on foundational studies which examined post-mortem tissue for histological signs of damage. This set of observations and the subsequently proposed limits to safe stimulation, termed the “Shannon limits,” allow for a simple calculation (using charge per phase and charge density) to determine the intensity of electrical stimulation that can be delivered safely to brain tissue. In the three decades since the Shannon limits were reported, advances in molecular biology have allowed for more nuanced and detailed approaches to be used to expand current understanding of the physiological effects of stimulation. Here, we investigated spatial transcriptomics as a new approach to assess the safety and efficacy of electrical stimulation in the brain. Electrical stimulation was delivered to the rat visual cortex with either acute or chronic electrode implantation procedures (acute: tissue collection 3 hours post-stimulation on the day of surgery; chronic: stimulation delivered 1-month post-implantation, and tissue collection 24 hours later). To explore the influence of device type and stimulation parameters, we used carbon fiber ultramicroelectrode arrays (7 µm diameter) and microwire electrode arrays (50 µm diameter) delivering charge and charge density levels selected above and below reported tissue damage thresholds (range: 2-20 nC, 0.1-1 mC/cm2). Spatial transcriptomics was performed using Visium Spatial Gene Expression Slides (10x Genomics), which enabled simultaneous immunohistochemistry and spatial transcriptomics to directly compare traditional histological metrics to transcriptional profiles within each tissue sample. Our data revealed unique spatial patterns of differentially expressed genes that are related to cellular processes including inflammation, cell cycle progression, and plasticity. Effects were dependent on stimulation parameters and were localized to both traditional and ultra-small device locations. The abundance of data gathered using this approach allows for sophisticated analysis that can be used to generate new hypotheses while also revealing novel potential biomarkers of neurostimulation.

citation:
  Whitsitt, Quentin A et al. “Spatial Transcriptomics as a Novel Approach to Redefine Electrical Stimulation Safety.” Frontiers in neuroscience vol. 16 937923. 19 Jul. 2022, doi:10.3389/fnins.2022.937923


dataset_id: STDS0000150
species: Homo sapiens
tissues: Pancreas
technologies: GeoMx DSP
disease: Pancreatic ductal adeno carcinoma
submission_date: 2022-03-21 00:00:00
last_modified: 2022-05-13 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199102
platforms: Illumina NovaSeq 6000 (Homo sapiens)
pmid: 35928007
title:
  Spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

summary:
  Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here we construct a high-resolution molecular landscape of the multicellular subtypes and spatial communities that compose PAC using single-nucleus RNA-seq and whole-transcriptome digital spatial profiling (SP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment-naïve. We uncovered expression programs across malignant cells and fibroblasts, including a newly-identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities: classical, squamoid-basaloid, and treatment-enriched. Our refined molecular and cellular taxonomy can advance precision oncology in PAC through stratification in clinical trials and as roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

overall_design:
  14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection

contributors:
  Hwang, William L;Jagadeesh, Karthik A;Guo, Jimmy A;Hoffman, Hannah I;Su, Jennifer;Shiau, Carina;Jacks, Tyler;Regev, Aviv

citation:
  Whitsitt, Quentin A et al. “Spatial Transcriptomics as a Novel Approach to Redefine Electrical Stimulation Safety.” Frontiers in neuroscience vol. 16 937923. 19 Jul. 2022, doi:10.3389/fnins.2022.937923


dataset_id: STDS0000172
title: Mouse olfactory sensory neurons, main olfactory epithelium and main olfactory bulb
species: Mus musculus
tissues: Neuron
organ_parts: Mature olfactory sensory neuron;Main olfactory epithelium;Main olfactory bulb
sex: F/M
technologies: scRNA;Slide-seqV2
disease: Olfactory bulb
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2021-03-16 00:00:00
last_modified: 2022-05-02 00:00:00
contributors: Wang, I-Hao
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169021
platforms: Illumina HiSeq 4000;Illumina NovaSeq 6000
pmid: 35314823
citation:
  Wang, I-Hao et al. “Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing.” Nature neuroscience vol. 25,4 (2022): 484-492. doi:10.1038/s41593-022-01030-8


dataset_id: STDS0000161
title: Reconstruction of the Mouse Olfactory Glomerular Map using Single-Cell Technologies
species: Mus musculus
tissues: Epithelium
organ_parts: Main olfactory epithelium
sex: male
technologies: MERFISH
disease: Olfactory bulb
submission_date: 2021-03-16 00:00:00
last_modified: 2022-05-02 00:00:00
contributors: Wang, I-Hao;Jiang, Hao-Ching;Park, Sung J;Liberman Greer, Paul
accessions: https://zenodo.org/record/5745947/
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 35314823
summary:
  The goal of scRNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR in a large and unbias scale. Olfactory epithelial single cell suspensions were made using 3 male and 3 female mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene). The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.ph

overall_design:
  Olfactory epithelial single cell suspensions made from 3 male and 3 female adult mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene)

citation:
  Wang, I-Hao et al. “Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing.” Nature neuroscience vol. 25,4 (2022): 484-492. doi:10.1038/s41593-022-01030-8


dataset_id: STDS0000142
title: Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb
species: Mus musculus
tissues: Brain
organ_parts: Olfactory bulb
development_stages: 4-6 months
sex: male
technologies: Slide-seqV2
disease: Olfactory bulb
submission_date: 2021-03-06 00:00:00
last_modified: 2022-05-02 00:00:00
contributors: Wang, I-Hao;Murray, Evan;Chen, Fei;Macosko, Evan Z;Liberman Greer, Paul
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169012
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 35314823
has_paired: STDS0000142
cell_types:
  celltype:Stage 2;celltype:Baseline;celltype:Glia;celltype:primary neuron;celltype:Stage 1;celltype:microglia

summary:
  The goal of spatial transcriptome analysis is to profile the glomeruli position representing different olfactory receptors. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals. All of the Slide-seqV2 procedures were performed as previously described

overall_design:
  Olfactory epithelial single cell suspensions made from 3 male and 3 female adult mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene)

citation:
  Wang, I-Hao et al. “Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing.” Nature neuroscience vol. 25,4 (2022): 484-492. doi:10.1038/s41593-022-01030-8


dataset_id: STDS0000177
title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]
species: Homo sapiens
tissues: Skin
organ_parts: Squamous Cell Carcinoma
technologies: Spatial Transcriptomics;10x Visium
disease: Skin carcinoma cancer
submission_date: 2020-01-24 00:00:00
last_modified: 2022-05-02 00:00:00
contributors: Ji, Andrew;Ji, Andrew L;Rubin, Adam J
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144239
platforms: Illumina NextSeq 500
pmid: 32579974
summary:
  To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and  site-matched normal skin

overall_design:
  Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing

citation:
  Ji, Andrew L et al. “Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.” Cell vol. 182,2 (2020): 497-514.e22. doi:10.1016/j.cell.2020.05.039


dataset_id: STDS0000223
species: Homo sapiens
tissues: Kidney
organ_parts: ccRCC tumor
technologies: 10x Visium
disease: renal cell cancer
submission_date: 2021-05-25 00:00:00
last_modified: 2022-04-19 00:00:00
contributors: Meylan, Maxime;de Reyniès, Aurélien;Sautès-Fridman, Catherine;Fridman, Wolf H
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175540
platforms: Illumina NovaSeq 6000
pmid: 35231421
has_paired: SCDS0000012
title:
  Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

summary:
  The presence of intratumoral tertiary lymphoid structures (TLS) is associated with positive clinical outcomes and responses to immunotherapy in cancer. Here, we used spatial transcriptomics to examine the nature of B cell responses within TLS in renal cell carcinoma (RCC). B cells were enriched in TLS, and therein, we could identify all B cell maturation stages toward plasma cell (PC) formation. B cell repertoire analysis revealed clonal diversification, selection, expansion in TLS, and the presence of fully mature clonotypes at distance. In TLS+ tumors, IgG- and IgA-producing PCs disseminated into the tumor beds along fibroblastic tracks. TLS+ tumors exhibited high frequencies of IgG-producing PCs and IgG-stained and apoptotic malignant cells, suggestive of anti-tumor effector activity. Therapeutic responses and progression-free survival correlated with IgG-stained tumor cells in RCC patients treated with immune checkpoint inhibitors. Thus, intratumoral TLS sustains B cell maturation and antibody production that is associated with response to immunotherapy, potentially via direct anti-tumor effects.

overall_design:
  Spatial transcriptomics of fresh frozen ccRCC human tumors
  *** Raw data has not been submitted at this time due to patient privacy concerns ***

citation:
  Meylan, Maxime et al. “Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer.” Immunity vol. 55,3 (2022): 527-541.e5. doi:10.1016/j.immuni.2022.02.001


dataset_id: STDS0000163
species: Mus musculus
tissues: Kidney
organ_parts: Cortex;Medulla;Renal pelvis
development_stages: 6 months
technologies: Slide-seqV2
disease: Normal atlas
submission_date: 2021-12-03 00:00:00
last_modified: 2022-04-07 00:00:00
contributors: Marshall, Jamie L;Noel, Teia;Wang, Qingbo S;Greka, Anna
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190094
platforms: Illumina NovaSeq 6000 (Mus musculus)
pmid: 35372810
title:
  High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

summary:
  High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and human kidneys, in healthy and in distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in human kidney by analyzing tissue from 9 distinct donors, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially-restricted kidney filter and blood flow regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially-restricted subpopulation of epithelial cells, we also found perturbations in 77 genes associated with the unfolded protein response (UPR), including Tmed9. Treatment with a TMED9-targeting compound showed efficient removal of toxic mutant proteins and reversal of the UPR. Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods and actionable targets.

overall_design:
  For the BTBR experiments, the BTBR-wt/wt are controls and BTBR-ob/ob are diabetic samples. Seven arrays per mouse and 4 mice of each gentoptype were processed. For the UMOD experiments, UMOD-WT are controls and UMOD-KI are ADTKD samples. Five arrays per mouse and 3 WT mice and 5 KI mice were processed. There are 3 separate files types: BAMs, raw data which is unmapped spatial data, and processed data which contains QCed and mapped kidney cell types.

citation:
  Marshall, Jamie L et al. “High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways.” iScience vol. 25,4 104097. 16 Mar. 2022, doi:10.1016/j.isci.2022.104097


dataset_id: STDS0000192
species: Mus musculus
tissues: Colon
sex: Female
technologies: 10x Visium
disease: Colon repair
submission_date: 2020-12-21 00:00:00
last_modified: 2022-03-09 00:00:00
contributors: Villablanca, Eduardo J;Frede, Annika;Sorini, Chiara;Tripathi, Kumar P
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163638
platforms: Illumina HiSeq 2500
pmid: 35149721
title:
  10X-single cell seq of IEC and Stroma during recovery after DSS colitis in B cell sufficient/deficient mice

summary:
  B cells expand during the recovery after DSS-induced colonic inflammation and might play a role in influencing tissue repair. To analyze the impact B cells might have on intestinal epithelial cells and stromal cells during recovery after intestinal injury the transcriptional profile of these mice was analysed in mice depleted of B cells and control mice on day 14 after DSS colitis.

overall_design:
  Female C57BL/6J mice were irradiated and received BM transplants with either CD19cre (ctrl) or CD19cre x iDTR cells. 8 weeks after BM transfer mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. On days 9, 10, 12 and 13 mice received i.p. injections of diphteria toxin (25ng/g BW) in PBS. On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 2) and submitted for sequencing.

citation:
  Parigi, Sara M et al. “The spatial transcriptomic landscape of the healing mouse intestine following damage.” Nature communications vol. 13,1 828. 11 Feb. 2022, doi:10.1038/s41467-022-28497-0


dataset_id: STDS0000139
title: A cellular resolution spatial transcriptomic landscape of the postnatal mouse brain
species: Mus musculus
tissues: Brain
development_stages: P7
technologies: Stereo-Seq
disease: Normal atlas
overall_design: The experiment were performed according to the standard protocol of Stereo-seq
submission_date: 2022-02-16 00:00:00
last_modified: 2022-02-16 00:00:00
contributors: Mengnan cheng;Liang Wu;Chuanyu Liu;Longqi Liu
contacts: wuliang2@genomics.cn
accessions: https://db.cngb.org/search/project/CNP0002646/;https://db.cngb.org/stomics/publications/35656552
platforms: DNBSEQ-T10
pmid: 35656552
cell_types:
  Fiber tract;Medulla and pons;Blood;LPO;CbXegr;CbXpu;Zona incerta;CbXigr;Meninge;CbWM;Ventricle;CbN;MRN;Superior collicular;Substantia nigra;L1;LHA;Stratum Hipp;L4-R;L2/3;VPrP;L6;L4-C;L5-C;Subiculum;DG;Thalamus;L5-R;SVZ;LPall;CA1;Reticular nucleus;CA2/3;Str-Cau;Pallidum;Str-OT;Str-ACB;AOV;OBs;OBi;SEZ

summary:
  Here we apply Stereo-seq to generate a spatially-resolved transcriptomic description of the postnatal day 7 (P7) murine whole brain sagittal section near the middle line. Our study comprehensively dissected the anatomical regions, gene expression and gene regulatory network patterns and cell type localization at whole brain scale.

citation:
  Cheng, Mengnan et al. “A Cellular Resolution Spatial Transcriptomic Landscape of the Medial Structures in Postnatal Mouse Brain.” Frontiers in cell and developmental biology vol. 10 878346. 17 May. 2022, doi:10.3389/fcell.2022.878346


dataset_id: STDS0000130
species: Mus musculus
tissues: Brain
sex: Male
technologies: 10x Visium
disease: Normal atlas
submission_date: 2022-01-25 00:00:00
last_modified: 2022-01-30 00:00:00
contributors: Ju, Huang
contacts: echoliub@sjtu.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194338
platforms: GPL24247
title:
  Excitatory SST neurons in the medial paralemniscal nucleus control repetitive self-grooming and encode reward

summary:
  We revealed that the MPLSST neurons are excitatory neurons releasing neurotransmitter  glutamate,and reveal that more than half of these neurons corelease neuropeptides SST and PTH2

overall_design:
  We performed a spatial transcriptomics analysis using the 10x Genomics Visium platform seeking to profile potentially informative markers in the MPL from a coronal section (close to bregma -4.72 mm) from post-natal day 60 (P60) male mice

citation:
  Sun, Jingjing et al. “Excitatory SST neurons in the medial paralemniscal nucleus control repetitive self-grooming and encode reward.” Neuron vol. 110,20 (2022): 3356-3373.e8. doi:10.1016/j.neuron.2022.08.010


dataset_id: STDS0000141
title: Spatially resolved multi-omics analytics of pituitary plasticity in mammals
species: Homo sapiens
tissues: Pituitary
development_stages: Adult
technologies: Stereo-Seq
disease: Normal atlas
submission_date: 2022-01-24 00:00:00
last_modified: 2022-01-24 00:00:00
contributors: Shang Liu;Chuqing Wang;Liang Wu;Yannan Cao
contacts: liushang@genomics.cn
platforms: DIPSEQ-T10
cell_types:
  Som (Somatotropes);Lac (Lactotropes);Thy (Thyrotropes);Gon (Gonadotropes);Cor (Corticotropes);PSC (Pituitary Stem Cells);GEC (Glandular Epithelial Cells);MSC (Mesenchymal Stromal Cells);EC (Endothelial Cell);Mic (Microglia);Ser (Serotonin);Mel (Melaotrope);CC (Cell Cycle);Axon (axonal projections of neuron);Pit (Pituicyte)

summary:
  Our results reveal the pituitary cell composition and spatial-temporal molecular features of mesenchymal, epithelial and stem cells, and hormonal cells. Analysis of pseudotime trajectory and transcription factor activity unveil the critical regulatory networks for cell fate determination and functions, including Axon guidance and Hippo pathways. The importance of endoplasmic reticulum stress and unfolded protein response in the regulation of oxidative stress, and enrichment of potent antioxidants in pituitary is identified. The plastic regulation of working, resting and multihormonal status for neuroendocrine cells is essential for the balance of pituitary hormones. Furthermore, the putative ligand-receptor interactions exhibit the regulatory relationships among diverse cell types, suggesting the pituitary stem cell niche comprising growth factors and extracellular matrix proteins. Our findings systematically illustrate the cellular and mechanistic basis of mammalian pituitary plasticity.

overall_design:
  we integrate omics data of the single-nucleus RNA and ATAC sequencing, high-resolution spatial transcriptomics, and metabolomics to investigate the cell diversity and plasticity in anterior pituitaries from adult human, monkey, and mouse. The single-cell transcriptomics of mouse pituitary organoids are analyzed. 


dataset_id: STDS0000118
title: Integrated analysis of single-cell and spatial transcriptomics in keloids
species: Homo sapiens
tissues: Skin
technologies: 10x Visium;scRNA
disease: Wound repair
submission_date: 2021-08-02 00:00:00
last_modified: 2022-01-23 00:00:00
contributors: Lee, Jong H;Shim, Joonho
contacts: bell711@hanmail.net
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181297
platforms: GPL21697;GPL24676
pmid: 35123990
summary:
  To uncover the underlying pathophysiology of keloids, we used two technologies, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). we focused on the molecular signature of keloids. In this study, we provide the comprehensive transcriptomic atlas of keloids and its matched spatial information, essential to understanding intercellular crosstalk in the skin microenvironments.

overall_design:
  We employed scRNA-seq on two keloid samples using the platform of 10X Genomics. To further assess the spatial heterogeneity and organization of keloid FBs, we performed ST analysis on tissue from keloid specimens (2 sections from 2 samples including one scRNA-seq paired sample). To confirm the study results, we further applied ST on two independent normal skin sections . Normal skin samples from skin cancer excision were used for ST analysis.

citation:
  Shim, Joonho et al. “Integrated Analysis of Single-Cell and Spatial Transcriptomics in Keloids: Highlights on Fibrovascular Interactions in Keloid Pathogenesis.” The Journal of investigative dermatology vol. 142,8 (2022): 2128-2139.e11. doi:10.1016/j.jid.2022.01.017


dataset_id: STDS0000114
species: Homo sapiens
tissues: Lung
technologies: 10x Visium
disease: Lung Normal atlas
overall_design: Spatial transcriptomics on normal human lung.
submission_date: 2021-06-16 00:00:00
last_modified: 2022-01-18 00:00:00
contacts: pt93@duke.edu, tata.lab@yahoo.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178361
platforms: GPL24676
pmid: 35355018
has_paired: STDS0000114
title:
  Spatially resolved transcriptomics revised human distal lung epithelial hierarchy [spatial transcriptomics]

summary:
  We performed spatial transcriptomics using 10x Genomic Visium Spatial Gene Expression on human lung.

contributors:
  Lakshminarasimha Murthy, Preetish K;Sontake, Vishwaraj;Tata, Aleksandra;Kobayashi, Yoshihiko;Tata, Purushothama Rao

citation:
  Kadur Lakshminarasimha Murthy, Preetish et al. “Human distal lung maps and lineage hierarchies reveal a bipotent progenitor.” Nature vol. 604,7904 (2022): 111-119. doi:10.1038/s41586-022-04541-3


dataset_id: STDS0000129
species: Mus musculus
tissues: Lung
sex: Male
technologies: 10x Visium
disease: Lung cancer
submission_date: 2022-01-11 00:00:00
last_modified: 2022-01-17 00:00:00
contributors: Rose, Samuel A;Dhainaut, Maxime;Brown, Brian D
contacts: brian.brown@mssm.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193460
platforms: GPL24247
pmid: 35290801
has_paired: SCDS0000013
title:
  Perturb-map coupled with spatial transcriptomics identifies mutation associated gene signatures in a mouse model of lung adenocarcinoma

summary:
  The cellular architecture of a tumor has a major impact on cancer outcome, and thus there is interest in identifying genes controlling the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a fibro-mucinous state and T-cells excluded, concomitant with upregulated TGFb and TGFb-mediated stroma activation, suggesting Tgfbr2 loss on lung cancer cells increased TGFb bioavailability and enhanced its suppressive effects on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.

overall_design:
  Male C57BL/6J mice were injected intravenously with KP (Kras G12D, p53 deleted) cells transduced with a Pro-Code/CRISPR library targeting 35 different genes associated with tumor-immune interaction. 10X Visium spatial transcriptomics profiling was performed on 4 separate sections of mouse lung from 3 different mice. Annotations for specific genes targeted in visium spots capturing tumor cells were generated by parallel hyperion imaging on a serial section to identify the linked protein barcode.

citation:
  Dhainaut, Maxime et al. “Spatial CRISPR genomics identifies regulators of the tumor microenvironment.” Cell vol. 185,7 (2022): 1223-1239.e20. doi:10.1016/j.cell.2022.02.015


dataset_id: STDS0000104
species: Arabidopsis thaliana
tissues: Leaf
organ_parts: Cauline leaf
development_stages: 6 weeks
technologies: Stereo-Seq
disease: Plants
submission_date: 2022-01-14 00:00:00
last_modified: 2022-01-14 00:00:00
contacts: xiakeke@genomics.cn
accessions: https://db.cngb.org/search/project/CNP0002618/
platforms: DNBSEQ-T10
pmid: 35512702
title:
  The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

cell_types:
  Upper epidermal cell;Lower epidermal cell;Palisade mesophyll cell;Spongy mesophyll cell;Guard cell;Vascular cell

summary:
  We present the first in situ single-cell transcriptome profiling in plant, scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing), which enabled the bona fide single-cell spatial transcriptome of Arabidopsis leaves.

overall_design:
  To enable in situ single-cell level transcriptome analysis in plant leaves, we set out to apply Stereo-seq in Arabidopsis. In this study, combining plant cell wall staining with high- resolution spatial transcriptomics using Stereo-seq, we present the first in situ single-cell transcriptome profiling in Arabidopsis leaves. Single-cell Stereo-seq (scStereo-seq) not only enables us to identify the main leaf cell types, but also allows us to distinguish cell sub-types, including upper and lower epidermal cell, palisade mesophyll cell and spongy mesophyll cell. Furthermore, we also show the existence of cell type-specific spatial gene expression gradients from main vein to leaf edge. We reconstructed those gradients to show for the first time the developmental trajectories of specific cell types according to their spatial distribution.

contributors:
  Keke Xia;Hai-Xi Sun;Jie Li;Jiming Li;Yu Zhao;Lichuan Chen;Chao Qin;Ruiying Chen;Guangyu Liu;Zhiyong Chen;Ruilian Yin;Bangbang Mu;Xiaojuan Wang;Mengyuan Xu;Xinyue Li;Yixin Qiao;Peisi Yuan;Shijie Hao;Jing Wang;Qing Xie;Jiangshan Xu;Shiping Liu;Yuxiang Li;Ao Chen;Longqi Liu;Ye Yin;Huanming Yang;Jian Wang;Ying Gu;Xun Xu

citation:
  Xia, Keke et al. “The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves.” Developmental cell vol. 57,10 (2022): 1299-1310.e4. doi:10.1016/j.devcel.2022.04.011


dataset_id: STDS0000128
title: Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
species: Mus musculus;Homo sapiens
tissues: Liver
technologies: 10x Visium;snRNA;CITE-seq
disease: Normal atlas
submission_date: 2021-12-29 00:00:00
last_modified: 2022-01-13 00:00:00
contacts: liesbet.martens@irc.vib-ugent.be
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE192741
platforms: GPL24247;GPL24676
pmid: 35021063
has_paired: STDS0000128
summary:
  Analysis of CITE-seq data , Nuclei RNA-seq data and single cell RNA-seq data on CD45+ and CD45- cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar), from healthy and steatotic human livers, from hamster liver, pig liver, chicken liver, monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers, NAFLD mouse livers, healthy human livers and steatotic human livers.

overall_design:
  Single cell RNA Seq = Liver CD45+ and CD45- cells derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar). Liver CD45+ and CD45- cells derived from healthy and obese humans.
  10 Visium Spatial Seq = mouse StSt liver, mouse StSt capsule, mouse NAFLD liver,  human non-steatotic liver, human steatotic liver.

contributors:
  Guilliams, Martin;Bonnardel, Johnny;Haest, Birthe;Vanderborght, Bart;Wagner, Camille;Remmerie, Anneleen;Bujko, Anna;Martens, Liesbet;Thoné, Tinne;Browaeys, Robin;De Ponti, Federico F;Vanneste, Bavo;Zwicker, Christian;Svedberg, Freya R;Vanhalewyn, Tineke;Gonçalves, Amanda;Lippens, Saskia;Devriendt, Bert;Cox, Eric;Ferrero, Giuliano;Wittamer, Valerie;Willaert, Andy;Kaptein, Suzanne F;Neyts, Johan;Dallmeier, Kai;Geldhof, Peter;Casaert, Stijn;Deplancke, Bart;ten Dijke, Peter;Hoorens, Anne;Vanlander, Aude;Berrevoet, Frederik;Van Nieuwenhove, Yves;Saeys, Yvan;Saelens, Wouter;Van Vlierberghe, Hans;Devisscher, Lindsey;Scott, Charlotte L

citation:
  Habenicht, Livia K L et al. “The C1q-ApoE complex: A new hallmark pathology of viral hepatitis and nonalcoholic fatty liver disease.” Frontiers in immunology vol. 13 970938. 6 Oct. 2022, doi:10.3389/fimmu.2022.970938


dataset_id: STDS0000062
title: Spatial transcriptome uncovers the mouse lung architectures and functions
species: Mus musculus
tissues: Lung
cell_types: alveolar type II;alveolar type I;vein;ciliated;artery;fibroblast
development_stages: 5 weeks
sex: Female
technologies: Stereo-Seq
disease: Normal atlas
overall_design: We applied Stereo-seq on a 5-week-old femal mouse following the manufacturer's protocol.
submission_date: 2022-01-11 00:00:00
last_modified: 2022-01-11 00:00:00
contributors: Yujia Jiang;Shijie Hao
contacts: haoshijie@genomics.cn
accessions: https://db.cngb.org/search/project/CNP0002590/
platforms: DNBSEQ-T10
pmid: 35391793
summary:
  Revealing the relationships between the tissue structures and transcriptomic information is significant for understanding the mechanisms and principles underpinning the biological processes in lung development and diseases. The widely transcriptomic technics, including bulk and single-cell RNA sequencing, cannot accurately restore the tissue location of the gene expression. The advanced spatial transcriptomic tools can fill this gap properly with in-situ RNA capturing and spatial barcode labeling and translating. However, the published spatial transcriptome data of lung is rare or low-quality. Here we harnessed the large-view and high-resolution capabilities of Stereo-seq, one of the most advanced spatial transcriptome tools, in a 5-week-old female mouse to uncover the lung functions with their tissue location resolved. We also found a gradient expression of a bunch of genes related to cell proliferation along the axis of the proximal-to-distal trachea. All the data provided by the study pave the way for further studies in lung development and disease in the future.

citation:
  Jiang, Yujia et al. “Spatial Transcriptome Uncovers the Mouse Lung Architectures and Functions.” Frontiers in genetics vol. 13 858808. 9 Mar. 2022, doi:10.3389/fgene.2022.858808


dataset_id: STDS0000061
title: Spatial transcriptomic profile of cervical squamous cell carcinoma
species: Homo sapiens
tissues: Cervical
organ_parts: Cervical tissue
cell_types: epithelial;fibroblast;endothelial (EC);myofibroblast;immune;Cancer;CAFs
sex: Female
technologies: Stereo-Seq
disease: Cervical squamous cell carcinoma
submission_date: 2021-12-30 00:00:00
last_modified: 2021-12-30 00:00:00
contributors: Xun Xu;Yanzhou Wang;Junhua Li;Peng Wu
contacts: pengwu8626@tjh.tjmu.edu.cn
accessions: https://db.cngb.org/stomics/project/STT0000015
platforms: DNBSEQ-T10
pmid: 35986392
summary:
  To understand the etiological, structural, and immunological characteristics of cervical squamous cell carcinoma (CSCC), we conducted spatial transcriptomics (ST) experiments  for cervical samples from 16 individuals.

overall_design:
  To understand the etiological, structural, and immunological characteristics of cervical squamous cell carcinoma (CSCC), we conducted spatial transcriptomics (ST) experiments  for cervical samples from 16 individuals.

citation:
  Ou, Zhihua et al. “Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma.” Advanced science (Weinheim, Baden-Wurttemberg, Germany) vol. 9,29 (2022): e2203040. doi:10.1002/advs.202203040


dataset_id: STDS0000119
title: Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain
species: Mus musculus
tissues: Brain
organ_parts: Coronal Brain
sex: Male
technologies: 10x Visium
disease: Brain injury
submission_date: 2021-08-14 00:00:00
last_modified: 2021-12-29 00:00:00
contributors: Buzzi, Raphael M;Akeret, Kevin;Hugelshofer, Michael;Schaer, Dominik J
contacts: raphael.buzzi@usz.ch
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182127
platforms: GPL24247
pmid: 34793930
summary:
  After intracranial hemorrhages, heme is released from cell-free hemoglobin. This red blood cell toxin may drive secondary brain injury at the hematoma-brain interface. This study aimed to generate a spatially resolved map of the transcriptome-wide gene expression changes in the heme-exposed brain and define the potential therapeutic activity of the heme-binding protein hemopexin.

overall_design:
  Spatial transcriptome analysis of mouse brain using the 10X genomics Visium spatial gene expression kit after stereotactic injections.

citation:
  Buzzi, Raphael M et al. “Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain.” Free radical biology & medicine vol. 179 (2022): 277-287. doi:10.1016/j.freeradbiomed.2021.11.011


dataset_id: STDS0000124
species: Mus musculus
tissues: Heart
technologies: 10x Visium
disease: Heart regeneration
submission_date: 2021-11-15 00:00:00
last_modified: 2021-12-23 00:00:00
contributors: Small, Eric M;Misra, Adwiteeya;Baker, Cameron
contacts: cameron_baker@urmc.rochester.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188888
platforms: GPL24247
pmid: 35050211
has_paired: SCDS0000015
title:
  Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]

summary:
  We use spatial transcriptomics to establish regional transcriptional profile of neonatal heart tissue obtained at indicated timpoints after apical resection surgery.

overall_design:
  The cardiac apex was resected at P2, within the regenerative window, and hearts were isolated at indicated timepoints for spatial transcriptomics.

citation:
  Misra, Adwiteeya et al. “Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics.” Journal of cardiovascular development and disease vol. 9,1 1. 21 Dec. 2021, doi:10.3390/jcdd9010001


dataset_id: STDS0000117
title: Comprehensive Atlas of the Mouse Urinary Bladder
species: Mus musculus
tissues: Bladder
technologies: 10x Visium
disease: Normal atlas
submission_date: 2021-07-14 00:00:00
last_modified: 2021-12-23 00:00:00
contributors: Dylan Baker;Paul Robson
contacts: baker@uchc.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180128
platforms: GPL21103
organ_parts:
  Whole Bladder Nuclear;Whole Mouse Bladder;Whole Bladder;Whole Mouse Bladder;Dissociated Mouse Bladder;Detrusor layer of bladder

summary:
  We report the application of single-cell based sequencing for high throughput profiling of the mouse urinary bladder. By utilizing multiple dissociation techniques and library preparation techniques we generated an atlas comprising 43,119 cells including major cell types absent from previous reports. We found that previous single-cell profiling of the mouse bladder lacked a major cell type in the detrusor smooth muscle and incorrectly annotated other cell types such as mesothelial cells. Using the atlas, we elucidated aspects of bladder biology including urothelial differentiation, the identity of interstitial cells of Cajal, detrusor smooth muscle control and immune distributions. Finally, we combine the single-cell based sequencing with spatial transcriptomics and imaging mass cytometry to add spatial context to transcriptomic profiling.

overall_design:
  Single cell and nucleus sequencing of the mouse urinary bladder paired with spatial transcriptomics and bulk RNA sequencing.

citation:
  Lemtiri-Chlieh, Fouad et al. “The hyperpolarization-activated, cyclic nucleotide-gated channel resides on myocytes in mouse bladders and contributes to adrenergic-induced detrusor relaxation.” American journal of physiology. Regulatory, integrative and comparative physiology vol. 323,1 (2022): R110-R122. doi:10.1152/ajpregu.00277.2021


dataset_id: STDS0000233
title: EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization
species: Mus musculus
tissues: Brain
technologies: EASI-FISH
submission_date: 2021-12-22 00:00:00
last_modified: 2021-12-22 00:00:00
pmid: 34875226
citation:
  Wang, Yuhan et al. “EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.” Cell vol. 184,26 (2021): 6361-6377.e24. doi:10.1016/j.cell.2021.11.024

accessions:
  https://janelia.figshare.com/articles/dataset/EASI-FISH_enabled_spatial_analysis_of_molecular_cell_types_in_the_lateral_hypothalamus/13749154


dataset_id: STDS0000060
title: High-resolution spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae
species: Drosophila melanogaster
tissues: Embryo
organ_parts: Embryo;Larvae
cell_types: midgut;carcass;fat body;epidermis;salivary gland;CNS;hindgut;hemolymph;muscle;trachea
technologies: Stereo-Seq
disease: Normal
submission_date: 2021-12-21 00:00:00
last_modified: 2021-12-21 00:00:00
contacts: liulongqi@genomics.cn
platforms: DNBSEQ-T1
pmid: 35512700
development_stages:
  Embryo of 14-16 h after egg laying;Embryo of 16-18 h after egg laying;1st instar larva;2nd instar larva;3rd instar larva

summary:
  This database is intended to curate 3D spatial transcriptomes of all stages of Drosophila embryos and larvae generated by Stereo-seq. Drosophila melanogaster strain w1118 embryos were collected at two late stages (14-16 h and 16-18 h after egg laying, corresponding to stage 16~17 of embryogenesis) and all three stages were also collected. These samples were subject to cryosection to generate 7~10 μm thick slices. All slices of each sample were applied to Stereo-seq chips to capture their 2D spatial transcriptomes. All the 2D spatial transcriptomes of each sample were combined to recreate their 3D spatial transcriptomes. More samples of different stages will be added in the future. With these data, one could visualize and analyze spatial expression patterns of genes of interest, 3D reconstruct tissue-specific spatial transcriptomes by clustering and annotation, simulate tissue developmental trajectory across development, identify cell signalling pathways and gene regulatory networks, examine gene functions in their intact spatial context etc.

contributors:
  Mingyue Wang;Qinan Hu;Tianhang Lv;Yuhang Wang;Rong Xiang;Qing Lan;Zhencheng Tu;Yanrong Wei;Kai Han;Yanru An

citation:
  Wang, Mingyue et al. “High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae.” Developmental cell vol. 57,10 (2022): 1271-1283.e4. doi:10.1016/j.devcel.2022.04.006

accessions:
  https://db.cngb.org/search/project/CNP0002189/;https://db.cngb.org/stomics/drosophila_melanogaster/3d/E14-16a;https://db.cngb.org/stomics/drosophila_melanogaster/3d/E16-18a;https://db.cngb.org/stomics/drosophila_melanogaster/3d/L1a;https://db.cngb.org/stomics/drosophila_melanogaster/3d/L2a;https://db.cngb.org/stomics/drosophila_melanogaster/3d/L3b;https://db.cngb.org/stomics/flysta3d/


dataset_id: STDS0000102
species: Mus musculus
tissues: Heart
development_stages: E13.5;E15.5
technologies: 10x Visium
disease: Heart failure
submission_date: 2021-07-03 00:00:00
last_modified: 2021-12-21 00:00:00
contributors: Tongbin Wu;Zhengyu Liang;Ju Chen
contacts: juchen@health.ucsd.edu
platforms: Illumina NovaSeq 6000
pmid: 34915728
title:
  PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (Spatial Transcriptomics)

summary:
  The loss of compact myocardial cardiomyocyte (compact CM) identity suggests that PRDM16 deficiency may dramatically alter the cellular composition in left ventricular (LV) compact myocardium. To test this hypothesis, we performed single-cell RNA-seq (scRNA-seq) to examine gene dysreulation in Prdm16cKO heart. We also performed Visium Spatial Transcriptomics (ST) to facilitate mapping CM clusters to their original locations in the heart. As a result, we were able to demonstrate gene misregulation in Prdm16cKO mouse mainly occurred in LV compact CM.

overall_design:
  Two pairs of Prdm16cKO/WT E13.5  mouse hearts and two pairs of Prdm16cKO/control E15.5  mouse hearts were used for Visium Spatial Transcriptomics (ST).

citation:
  Wu, Tongbin et al. “PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle.” Circulation vol. 145,8 (2022): 586-602. doi:10.1161/CIRCULATIONAHA.121.056666

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179392;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179390


dataset_id: STDS0000116
title: Human prostate luminal epithelia adopt a club-like state in response to low androgen levels
species: Homo sapiens
tissues: Prostate
technologies: 10x Visium
disease: Prostate injury
submission_date: 2021-06-25 00:00:00
last_modified: 2021-12-18 00:00:00
contributors: Strand, Douglas W;Henry, Gervaise H
contacts: gervaise.henry@utsouthwestern.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178934
platforms: GPL24676
pmid: 34928497
has_paired: SCDS0000017
summary:
  Spatial transcriptomics of treatment naive and 5-alpha reductase inhibitior treated human BPH tissue

overall_design:
  Fresh human prostate specimens were embedded in OCT, slides were H&E stained and processed for 10x Genomics Visium spatial transcriptomics.

citation:
  Joseph, Diya B et al. “5-Alpha reductase inhibitors induce a prostate luminal to club cell transition in human benign prostatic hyperplasia.” The Journal of pathology vol. 256,4 (2022): 427-441. doi:10.1002/path.5857


dataset_id: STDS0000140
title: Macaque Brain Atlas
species: Macaca fascicularis
tissues: Brain
technologies: Stereo-Seq
disease: Normal atlas
submission_date: 2021-12-16 00:00:00
last_modified: 2021-12-16 00:00:00
platforms: DNBSEQ-T10
pmid: 36347848
summary:
  Non-human primates provide a unique way to study the only model in which both developmental and pathological features of the brain in a species phylogenetically close to human. In the past decade, breakthrough advances in single-cell sequencing have enabled the mapping of cell taxonomy and heterogeneity in the developing and adult brain of different mammalian species. Here, we generated single-cell chromatin accessibility (single-cell ATAC) and transcriptomic data of 358,237 cells from three cortical regions of the adult cynomolgus monkey Macaca fascicularis brain. We then integrated this dataset with Stereo-seq (Spatio-Temporal Enhanced Resolution Omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular and regulatory states.

citation:
  Lei, Ying et al. “Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex.” Nature communications vol. 13,1 6747. 8 Nov. 2022, doi:10.1038/s41467-022-34413-3

accessions:
  https://db.cngb.org/mba;https://db.cngb.org/search/project/CNP0000927/;https://db.cngb.org/stomics/publications/36347848


dataset_id: STDS0000115
species: Mus musculus
tissues: Heart
technologies: 10x Visium
disease: Heart failure
submission_date: 2021-06-23 00:00:00
last_modified: 2021-12-14 00:00:00
contributors: David Zemmour;Rebecca A Porritt;Magali N Rivas;Moshe Arditi
contacts: davidpz@fas.harvard.edu, david.puyraimond@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178799
platforms: GPL24247
pmid: 34517723
title:
  Spatial transcriptomics (Visium, Spatial 3' V1, 10x Genomics) analysis of heart tissues in a murine model of Kawasaki disease vasculitis

summary:
  Spatial transcriptomics (Visium, Spatial 3' V1, 10x Genomics) analysis of heart tissues from Lactobacillus casei cell wall extract (LCWE)-injected mice and control PBS-injected mice

overall_design:
  Heart from one LCWE-injected and one PBS-injected mice were harvested one week after injection and sectioned to 10碌m and used for Visium Spatial Transcriptomics 3' V1

citation:
  Porritt, Rebecca A et al. “NLRP3 Inflammasome Mediates Immune-Stromal Interactions in Vasculitis.” Circulation research vol. 129,9 (2021): e183-e200. doi:10.1161/CIRCRESAHA.121.319153


dataset_id: STDS0000111
species: Mus musculus
tissues: Colon
technologies: 10x Visium
disease: Colon regeneration and repair
submission_date: 2021-03-26 00:00:00
last_modified: 2021-12-07 00:00:00
contributors: Srustidhar Das;Eduardo Villablanca;Ludvig Larsson
contacts: ludvig.larsson@scilifelab.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169749
platforms: GPL21103
pmid: 35149721
has_paired: SCDS0000038
title:
  10X Visium Spatial transcriptomics of murine colon in steady state and during recovery after DSS colitis

summary:
  The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon in steady state and during mucosal healing upon dextran sodium sulfate (DSS) induced injury

overall_design:
  Wild type C57BL/6J mice were exposed to DSS in drinking water for 7 days and then allowed to recover for 7 more days. Mouse colonic tissues were collected either on day 0 (without any exposure to DSS) or on day14 after exposure to DSS, Swisrolled and frozen in OCT. Mouse colonic tissues (day0 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide. Samples were processed according to 10X Visium spatial transcriptomics protocol and submitted for sequencing.

citation:
  Parigi, Sara M et al. “The spatial transcriptomic landscape of the healing mouse intestine following damage.” Nature communications vol. 13,1 828. 11 Feb. 2022, doi:10.1038/s41467-022-28497-0


dataset_id: STDS0000194
title: 10X-single cell seq of B cells during colitis (d0 and d14)
species: Mus musculus
tissues: Colon
sex: Female
technologies: 10x Visium
disease: Colon repair
submission_date: 2020-12-21 00:00:00
last_modified: 2021-12-07 00:00:00
contributors: Villablanca, Eduardo J;Frede, Annika;Sorini, Chiara;Tripathi, Kumar P
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163637
platforms: Illumina HiSeq 2500
pmid: 36462502
summary:
  B cells expand during the recovery after DSS-induced colonic inflammation. To investigate if a specific subtype is expanding and to analyse the transcriptional profile of these cells a transcriptional analysis on single cell level was carried out. In detail,  B cells were isolated from the colon of mice on day 0 (no treatment) or day 14 (recovery) after 7 days of DSS treatment by flow cytometric sorting and analyzed by 10X sequencing.

overall_design:
  Female C57BL/6J mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. Lymphocytes were isolated from the colonic lamina propria on day 0 (ctrl) and day 14 (recovery) and B cells were sorted using flow cytometry. Afterwards cells were processed according to 10x Genomics protocol for Chromium Single cell 3’ kit (version 2) and submitted for sequencing

citation:
  Frede, Annika et al. “B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing.” Immunity vol. 55,12 (2022): 2336-2351.e12. doi:10.1016/j.immuni.2022.11.002


dataset_id: STDS0000126
species: Mus musculus
tissues: Heart
organ_parts: Heart;Ileum
technologies: 10x Visium
disease: Heart failure
submission_date: 2021-11-26 00:00:00
last_modified: 2021-12-05 00:00:00
contributors: Madhav Mantri;Meleana M Hinchman;John L Parker;Iwijn De Vlaminck
contacts: id93@cornell.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189636
platforms: GPL21103
pmid: 36970396
title:
  Time-course single-cell and spatial transcriptomics of reovirus-induced myocarditis in neonatal mice

summary:
  A significant fraction of sudden death in young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used single-cell and spatially resolved RNA sequencing (RNA-seq) to study the cellular and spatial  heterogeneity of myocarditic processes in the hearts of reovirus-infected neonatal mice at multiple predetermined time points after initial infection at the primary site of infection. We further applied these technologies to study the innate response to reovirus infection in the intestine. In addition, we performed time-dependent single-cell RNA-seq (scRNA-seq) of cardiac tissues of mice infected with a reovirus point mutant that does not cause myocarditis. To establish viral tropism, we implemented molecular enrichment of non-polyadenylated viral transcripts that were otherwise poorly represented in the transcriptomes. Our measurements give insight into the cardiac cell-type specificity of innate immune responses, into the tropism of the virus in the intestine and the heart, and into the transcriptional states of cell types involved in the production of inflammatory cytokines and the recruitment of circulating immune cells. Analyses of spatially restricted gene expression in myocarditic regions and the border zone around those regions identified injury and stress responses in different cell types, including cardiomyocytes. Overall, our data identify spatially restricted cellular interactions and cell-type specific host responses during reovirus-induced myocarditis.

overall_design:
  Time-course single-cell and spatial transcriptomics of ileum and heart tissues from reovirus-infected neonatal mice

citation:
  Mantri, Madhav et al. “Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.” Nature cardiovascular research vol. 1,10 (2022): 946-960. doi:10.1038/s44161-022-00138-1


dataset_id: STDS0000122
title: Spatial transcriptomic studies of the small intestine from WT and DDX5△IEC (KO) mice
species: Mus musculus
tissues: Intestine
technologies: 10x Visium
disease: Normal atlas
submission_date: 2021-09-21 00:00:00
last_modified: 2021-12-03 00:00:00
contributors: Long, Tianyun;Lemolo, Attilio;Telese, Francesca;Huang, Wendy M
contacts: wjh003@ucsd.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184564
platforms: GPL24247
pmid: 34853057
summary:
  DDX5, a DEAD box containing RNA binding protein, is involved in multiple aspects of RNA metabolism and is abundantly expressed in all subsets of the intestinal epithelial cells (IEC). Here, we characterized the DDX5-dependent transcriptome in the small intestine. In the DDX5△IEC tissue, we found that secretory IEC lineage progenitor containing spots (Atoh1hi and Sox4hi) had reduced expression of Pou2f3, a master regulator of a subset of IECs called tuft cells. As a result of the loss of Pou2f3 expression in the progenitors, DDX5△IEC tissue harbored lower number of tuft cell containing spots (Dclk1hi) compare to WT tissues.

overall_design:
  One intestine tissue from each genotype were obtained from 8wk old cohoused mice. Results of ileum epithelium from DDX5鈻矷EC mutant mice were compared to those from WT mice.

citation:
  Long, Tianyun et al. “RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.” Gut vol. 71,9 (2022): 1790-1802. doi:10.1136/gutjnl-2021-324984


dataset_id: STDS0000125
species: Homo sapiens
tissues: Lung
technologies: 10x Visium
disease: Lung cancer development
submission_date: 2021-11-24 00:00:00
last_modified: 2021-12-02 00:00:00
contributors: Tao Jiang;Shiquan Sun;Yue Fan;Jianfei Zhu
contacts: xafanyue@xjtu.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189487
platforms: GPL21103
pmid: 36434043
title:
  Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [ST]

summary:
  To illuminate the evolutionary trajectory of LUAD from AIS to IAC, high-throughput scRNA-seq and ST data were generated and integrated to create a large-scale, single-cell spatiotemporal atlas of LUAD. We compiled a multi-omics atlas of the early-stage LUAD invasion process that reflects the heterogeneity of cancer cells, the competitive polyclonal origin of LUAD, signalling interactions between cancer cells and the TME, and the pseudo-chronological nature of LUAD invasion. The spatial distribution characteristics of LUAD cells revealed the spatial heterogeneity of LUAD and the mechanism of spatial immune escape in LUAD, which provides strong evidence supporting clinical diagnosis and surgical intervention at the single-cell level.

overall_design:
  Nine resected samples (TD1-9, three each from AIS, MIA and IAC cases) from nine treatment-na茂ve patients were collected for droplet-based scRNA-seq. In parallel, six paired samples were subjected to ST

citation:
  Zhu, Jianfei et al. “Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics.” Experimental & molecular medicine vol. 54,11 (2022): 2060-2076. doi:10.1038/s12276-022-00896-9


dataset_id: STDS0000103
species: Homo sapiens
tissues: Liver
technologies: 10x Visium
disease: Liver injury regeneration
submission_date: 2021-10-06 00:00:00
last_modified: 2021-12-02 00:00:00
contributors: Tallulah S Andrews;Jawairia Atif;Jeff C Liu;Sonya MacParland
contacts: tallulandrews@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185477
platforms: Illumina HiSeq 2500
pmid: 34792289
has_paired: STDS0000103
title:
  Single-Cell, Single-Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

summary:
  Comparison of single cell RNAseq and single nucleus RNAseq on four healthy human liver caudate lobes, with cell-types validated using one slice of a fifth healthy human for VISIUM Spatial Transcriptomics. Raw UMI count tables can be found here: https://figshare.com/projects/Human_Liver_SC_vs_SN_paper/98981
  Processed Seurat Objects can be found here:
  https://www.dropbox.com/sh/sso15ehqmrrh6mk/AACKHOsSlZW0_Zy9cbCkOmMfa?dl=0

overall_design:
  Four healthy human liver caudate lobes were removed prior to transplantation into living recipients. A potion of each lobe was frozen then nuclei were extracted and sequenced with 10x Chromium while another portion was dissociated immediately while still fresh and isolated cells were sequenced with 10x Chromium.

citation:
  Andrews, Tallulah S et al. “Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity.” Hepatology communications vol. 6,4 (2022): 821-840. doi:10.1002/hep4.1854


dataset_id: STDS0000200
title: Spatial RNA sequencing of regenerating mouse hindlimb muscle
species: Mus musculus
tissues: Muscle
organ_parts: Tibialis anterior muscle
development_stages: 5 months
sex: Female
technologies: 10x Visium
disease: Muscle regeneration
submission_date: 2020-11-12 00:00:00
last_modified: 2021-12-02 00:00:00
contributors: McKellar, David William;McKellar, David W;Cosgrove, Benjamin D;De Vlaminck, Iwijn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161318
platforms: Illumina NextSeq 500
pmid: 34773081
summary:
  We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.

overall_design:
  Tibialis anterior muscles were injected with notexin and collected two, five, and seven days post-injury. Samples were frozen in OCT. 10 micron tissue sections were assayed using the Visium Spatial Gene Expression Kit (v1). To improve resolution, each spot within the Visium slide was deconvolved using a matched single-cell RNA sequencing reference and BayesPrism (https://github.com/Danko-Lab/TED). Cell type fractions for each spot are included in the metadata files.

citation:
  McKellar, David W et al. “Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.” Communications biology vol. 4,1 1280. 12 Nov. 2021, doi:10.1038/s42003-021-02810-x


dataset_id: STDS0000121
title: Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model
species: Mus musculus
tissues: Kidney
sex: Female
technologies: 10x Visium
disease: Kidney injury
submission_date: 2021-08-27 00:00:00
last_modified: 2021-11-23 00:00:00
contributors: Dixon, Eryn E;Wu, Haojia;Muto, Yoshiharu;Wilson, Parker C;Humphreys, Benjamin D
contacts: d.eryn@wustl.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182939
platforms: GPL24247
pmid: 34853151
has_paired: SCDS0000039
summary:
  We optimized and validated a female bilateral ischemia reperfusion injury model. Using the 10X Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. An ischemia time of 34 minutes in a female murine model resulted in comparable injury to males across the time course of injury and repair. We report increased resolution of cell and gene expression with Giotto, a computational toolbox for spatial data analysis. Using a seeded non-negative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we find that injured proximal tubule cells are characterized by increasing macrophage and lymphocyte interactions even at 6 weeks after injury, consistent with a pro-inflammatory role for this cell state. In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created a data visualization web application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/).

overall_design:
  10X Visium was used to create a transcriptomic atlas of female kidney injury to discover, validate, and define spatial and temporal expression of injury specific genes.

citation:
  Dixon, Eryn E et al. “Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model.” Journal of the American Society of Nephrology : JASN vol. 33,2 (2022): 279-289. doi:10.1681/ASN.2021081150


dataset_id: STDS0000123
title: Fundamentals of Vaping-Associated Pulmonary Injury Leading to Severe Respiratory Distress [Visium]
species: Mus musculus
tissues: Lung
organ_parts: Upper pulmonary brances
sex: F/M
technologies: 10x Visium
disease: Pulmonary Injury
submission_date: 2021-11-15 00:00:00
last_modified: 2021-11-20 00:00:00
contributors: Sussman, Mark A;Echeagaray, Oscar E;Esquer, Carolina
contacts: oscar.echeagaray@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188805
platforms: GPL24247
pmid: 34810278
summary:
  Spatial transcriptomic (10X Genomics Visium) to profile pulmonary branches from Non-Vaped (NV) and Vaped (V) mice.

overall_design:
  Spatial Transcriptional profiling of  upper pulmonary brances of Non-Vaped (NV) and Vaped (V) mice by gene expression slides approach using 10X Genomics Visium Platform

citation:
  Esquer, Carolina et al. “Fundamentals of vaping-associated pulmonary injury leading to severe respiratory distress.” Life science alliance vol. 5,2 e202101246. 22 Nov. 2021, doi:10.26508/lsa.202101246


dataset_id: STDS0000120
title: Dietary palmitic acid promotes a prometastatic memory based on Schwann Cell activation
species: Mus musculus;Homo sapiens
tissues: Tumor
technologies: 10x Visium
disease: Metastasis
submission_date: 2021-08-26 00:00:00
last_modified: 2021-11-19 00:00:00
contributors: Marc E Bayes;Gloria P Angulo;Salvador A Benitah;Holger Heyn
contacts: aberenguerl@tauli.cat
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182867
platforms: GPL21103
pmid: 34759321
has_paired: STDS0000120
summary:
  Metastasis is promoted by fatty acid (FA) uptake and metabolism 1-2 . How this works, or whether all dietary FAs are prometastatic, is not known. Here we show that dietary palmitic acid (PA), but not oleic acid (OA) or linoleic acid, promotes metastasis in oral carcinomas and melanoma, indicating specificity of action for distinct FAs. Strikingly, tumours acutely exposed to a PA–rich diet remain highly metastatic even when serially transplanted. This PA–induced prometastatic memory requires the FA transporter CD36 as well as the epigenetically stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A/COMPASS. Bulk, single cell and positional RNA sequencing indicate that genes with this metastatic memory predominantly relate to a neural  signature that stimulates activation of intratumor Schwann cells and perineural invasion, two parameters strongly correlated with metastasis but etiologically poorly understood 3-4 . Mechanistically, tumour-associated Schwann cells secrete a specialized pro-regenerative extracellular matrix reminiscent of perineuronal nets, which when ablated strongly inhibits metastatic colonization. The induction of the epigenetic neural signature and its associated long-term boost in metastasis downstream of PA require the transcription factor EGR2 and the glial cell-stimulating peptide galanin. We provide evidence for a long-term epigenetic stimulation of metastasis by a dietary metabolite related to a pro-regenerative state of tumour-activated Schwann cells. In addition to underscoring the potential danger of eating large amounts of PA, our results reveal novel epigenetic and neural-related therapeutic strategies for metastasis.

overall_design:
  Single-cell RNA sequencing and Visium Spatial Transcriptomics was used to explore changes in the tumor microenvironment in response to a fatty acid rich diet. Samples from mouse models under control and palmitic acid rich diets in control and CD36 knockouts.

citation:
  Pascual, Gloria et al. “Dietary palmitic acid promotes a prometastatic memory via Schwann cells.” Nature vol. 599,7885 (2021): 485-490. doi:10.1038/s41586-021-04075-0


dataset_id: STDS0000105
title: Single-cell analysis of the aging female mouse hypothalamus
species: Mus musculus
tissues: Brain
organ_parts: hypothalamus
development_stages: P56;Adult
sex: Female
technologies: 10x Visium
disease: Brain Hypothalamus
overall_design: individual
submission_date: 2021-11-12 00:00:00
last_modified: 2021-11-12 00:00:00
contributors: Vitalii Kleshchevnikov
contacts: vk7@sanger.ac.uk
accessions: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11114/
summary:
  We developed cell2location, a principled and versatile Bayesian model that is designed to resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. To validate cell2location in real tissue, we applied the model to data from the mouse brain, which features diverse neural cell types organised in a well characterised spatial architecture across brain areas, thus presenting a canonical use case to test spatial genomics. We generated matched single nucleus (sn, this submission) and Visium spatial RNA-seq (10X Genomics) profiles of adjacent mouse brain sections that contain multiple regions from the telencephalon and diencephalon. To assess the biological and intra-organ technical variation in spatial mapping, we assayed two mouse brains and serial tissue sections from each brain (total of 3 and 2 matched sections from two animals, respectively, and an extra section for snRNA-seq), creating a rich multi-modal and replicated transcriptomic dataset.  Tissue processing. Brains of wild-type adult C57BL/6 mice (postnatal day 56, 1 female and 1 male) were dissected, snap frozen, embedded in optimal cutting temperature compound (Tissue-Tek) and stored at -80oC. Brain hemispheres were cryosectioned at -20oC using a cryostat (Leica, CM3050S). To assess tissue quality, RNA was extracted from test tissue sections using the RNeasy Pico Kit (Qiagen) and yielded high RIN values (9.6 and 9.7) on an Agilent Bioanalyser, indicating high RNA quality.  For matched single nuclei and Visium RNA-seq experiments, brain hemispheres were cryosectioned to adjacent thick (200 µm) and thin (10 µm) coronal sections, respectively, and processed the same day. In total, four consecutive sets of thick and thin tissue sections were collected from each brain. Five sets of tissue sections yielded both good quality single nuclei and Visium data (three adjacent sections from mouse 1 and two sections from mouse 2) while one additional section from mouse 2 yielded good single nuclei; these were considered for analysis in this study.   Visium spatial transcriptomics. Thin (10 µm) mouse brain sections were cryosectioned and mounted directly onto separate capture areas on 10X Visium Spatial Gene Expression slides (beta product version). Processing was done per manufacturer’s protocols. Briefly, sections were methanol-fixed, hematoxylin and eosin (H&E)-stained, and imaged on a NanoZoomer 2.0 slide scanner (Hamamatsu). Sections were then permeabilized and further processed to obtain cDNA libraries that were quality controlled using the Agilent Bioanalyser. The cDNA libraries were sequenced on the Illumina HiSeq 4000 system, aiming at 300 million raw reads per section with read lengths 28cy R1, 8cy i7 index, 0cy i5 index, 91cy read 2.  10X Visium spatial sequencing data was aligned to mouse pre-mRNA genome reference version mm10 using 10X SpaceRanger and mRNA count matrices were generated by adding intronic and exonic reads for each gene in each location. The paired histology H&E images were processed using 10X SpaceRanger to select locations covered by tissue by aligning pre-recorded spot locations with fiducial border spots in the histology image. This allows evaluating the correspondence between cell maps produced using our method and the known brain anatomy. This also allows identifying the number of nuclei in each spot using nuclear segmentation as described in Suppl. Methods and reported in Fig S8A-D. The histology image was used to manually annotate cortical layers in the primary somatosensory cortex (SSp) region using the lasso tool in the 10X Loupe browser.

citation:
  Hajdarovic, Kaitlyn H et al. “Single-cell analysis of the aging female mouse hypothalamus.” Nature aging vol. 2,7 (2022): 662-678. doi:10.1038/s43587-022-00246-4


dataset_id: STDS0000097
title: Spatial transcriptomics of healing and non-healing diabetic foot ulcers
species: Homo sapiens
tissues: Skin
development_stages: 59 days;50 days
technologies: GeoMx DSP
disease: Wound repair
submission_date: 2021-02-03 00:00:00
last_modified: 2021-10-30 00:00:00
contributors: Georgios Theocharidis;Aristidis Veves
contacts: aveves@bidmc.harvard.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166120
platforms: GPL21697
pmid: 35013299
summary:
  Diabetic foot ulcers (DFUs) are a devastating complication of diabetes. To better understand the molecular mechanisms and cell types implicated in DFU healing, we used NanoStringâ€™s GeoMx Digital Spatial profiling platform on DFU tissue sections and compared gene expression of areas within the same ulcer as well as between patients who in 12 weeks following surgery healed their DFU (Healers, N=2) vs those who did not (Non-Healers, N=2).

overall_design:
  The spatial transcriptome profiling was performed using NanoString芒鈧劉s GeoMx Digital Spatial profiling platform on unfixed frozen 5 脦录m tissue sections. Samples were  processed as  follows: 1) 10% neutral buffered formalin fixation overnight, 2) target retrieval (1X Tris EDTA, pH 9.0 for 20 min), 3) proteinase K digestion (1 脗碌g/mL for 15 min), 4) post-fixation (10% NBF, Tris-glycine stop buffer), 5) in-situ hybridization overnight with the GeoMx Cancer Transcriptome Atlas probe panel (1800-plex), 6) stringent washes (50:50 formamide/4X SSC), and 7) fluorescent antibody/marker (aSMA, Clone: 1A4, Abcam; CD45, Clone: 2B11+PD7/26, Novus; PanCK, Clone: AE1/AE3, Novus) incubation, 1 hour at room temperature. Sections were then loaded onto the GeoMx脗庐 Digital Spatial Profiler. For profiling, circular regions of interest (ROIs), approximately 500 脦录m in diameter, located within the ulcers or in neighboring non-ulcerated tissue were selected to include high concentrations of CD45+ immune cells in close proximity to vessels (aSMA+ structures). After ROI selection, the GeoMx instrument illuminated each ROI separately with UV light to cleave, aspirate, and deposit the oligonucleotides from the hybridized ISH probes for downstream sequencing into a 96-well plate.

citation:
  Theocharidis, Georgios et al. “Single cell transcriptomic landscape of diabetic foot ulcers.” Nature communications vol. 13,1 181. 10 Jan. 2022, doi:10.1038/s41467-021-27801-8


dataset_id: STDS0000093
title: Spatial transcriptome analysis of gastric cancer which GAN-KP transplanted C57BL/6J mouse
species: Mus musculus
tissues: Stomach
organ_parts: GAN-KP tumor
technologies: 10x Visium
disease: Gastric cancer
submission_date: 2021-10-20 00:00:00
last_modified: 2021-10-24 00:00:00
contributors: Juntaro Yamasaki;Yuki Hirata;Hideyuki Saya;Osamu Nagano
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186290
platforms: GPL17021
pmid: 34931404
has_paired: SCDS0000014
summary:
  We have now developed an organoid-based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN-p53KO) organoids and KRASG12V-expressing GAN-p53KO (GAN-KP) organoids were generated by genetic manipulation of GAN mouseâ€“derived tumor (GAN-WT) organoids. To uncover the molecular mechanism underlying the intratumoral heterogeneity of GAN-KP tumors, we performed spatial transcriptomics analysis with the 10Ã— Genomics Visium platform, which allows characterization of the spatial topography of gene expression.

overall_design:
  GAN-KP cells were transplanted into the stomach wall of mice and gene expression was analyzed two weeks later.

citation:
  Yamasaki, Juntaro et al. “MEK inhibition suppresses metastatic progression of KRAS-mutated gastric cancer.” Cancer science vol. 113,3 (2022): 916-925. doi:10.1111/cas.15244


dataset_id: STDS0000058
title: MOSTA: Mouse Organogenesis Spatiotemporal Transcriptomic Atlas
species: Mus musculus
tissues: Embryo
technologies: Stereo-Seq
disease: Embryonic development
submission_date: 2021-10-22 00:00:00
last_modified: 2021-10-22 00:00:00
accessions: https://db.cngb.org/search/project/CNP0001543/;https://db.cngb.org/stomics/mosta/
platforms: DNBSEQ-T1
pmid: 35512705
summary:
  We have only begun to scratch the surface in understanding mammalian development. An overwhelming caveat is the lack of topographical transcriptomic information to correlate signaling cues and cell-cell interactions within the hierarchy of cell fate decisions. Spatially resolved transcriptomic technologies are promising tools to fill this gap. However, the small field of view and imbalance between resolution and transcript capture of current methodologies precludes their systematic application to study relatively large and multilayered embryos. Here, we have combined DNA nanoball (DNB) patterned arrays and in situ RNA capture to create SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq). This approach allows transcriptomic profiling of large histological sections with high resolution, sensitivity, and reproducibility. We have applied Stereo-seq to study the kinetics of transcriptional variation, the networks of transcription factor binding events and their relationship with morphogens across spatial domains of gene expression in a time course of mouse organogenesis. We have used this information to detect the emergence of tissue-specific cell identities such as early neuroblast populations in the late neural tube stage or the gradients of neuronal specification in the neocortex. Furthermore, we have mapped the expression of a panel of developmental disease-related loci to define the spatiotemporal windows of tissue vulnerability. Our panoramic atlas constitutes a essential resource to investigate longstanding questions concerning the molecular basis of normal and abnormal mammalian development.

citation:
  Chen, Ao et al. “Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.” Cell vol. 185,10 (2022): 1777-1792.e21. doi:10.1016/j.cell.2022.04.003


dataset_id: STDS0000131
title: Human Prostate Cancer, Acinar Cell Carcinoma (FFPE)
species: Homo sapiens
tissues: Prostate
technologies: 10x Visium
disease: Prostate cancer
submission_date: 2021-10-09 00:00:00
last_modified: 2021-10-09 00:00:00
has_paired: SCDS0000005
accessions:
  https://www.10xgenomics.com/resources/datasets/human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard


dataset_id: STDS0000098
title: Spatial transcriptomics of Cutaneous and Systemic Lupus Erythematosus skin
species: Homo sapiens
tissues: Skin
technologies: GeoMx DSP
disease: Wound repair
submission_date: 2021-08-26 00:00:00
last_modified: 2021-10-02 00:00:00
contributors: Richmond JM;Deng A
contacts: lzhang@nanostring.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182825
platforms: GPL24676
summary:
  We performed spatial transcriptomics on a case series of different clinical subtypes of cutaneous lupus erythematosus including acute cutaneous lupus erythematosus (malar rash, systemic lupus erythematosus). Our goals were to (1) determine which differentially expressed genes (DEGs) could be attributed to specific cell populations in specific locations within the tissue, (2) determine if spatial transcriptomics could better distinguish between CLE clinical subtypes than bulk RNA approaches and (3) examine potential cell-cell communication pathways within the skin lesions.

overall_design:
  NanoString Digital Spatial Profiling (DSP) with Whole Transcriptome Atlas (WTA) was performed on 4 chronic/discoid lupus erythematosus (CCLE/DLE), 3 subacute cutaneous lupus erythematosus (SCLE) and 3 acute cutaneous lupus erythematosus (ACLE/SLE) patient skin biopsies compared to 3 healthy controls (skin cancer excision healthy/clear margins).


dataset_id: STDS0000091
species: Mus musculus
tissues: Skeleton
organ_parts: Sagittal suture
development_stages: P0
technologies: 10x Visium
disease: Normal atlas
submission_date: 2021-05-12 00:00:00
last_modified: 2021-10-01 00:00:00
contributors: Thomas L Clemens;Aaron W James;Robert J Tower
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174313
platforms: GPL13112
pmid: 34663698
title:
  Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGFÎ² signaling

summary:
  The patterning and ossification of the mammalian skeleton requires the coordinated actions of both intrinsic bone morphogens and extrinsic neurovascular signals, which function in a temporal and spatial fashion to control mesenchymal progenitor cell (MPC) fate. Here we show genetic inhibition of Tropomyosin receptor kinase A (TrkA) sensory nerve innervation of the developing cranium results in premature calvarial suture closure, associated with a decrease in suture MPC proliferation. In vitro, axons from peripheral afferent neurons derived from DRGs of wild type mice induce MPC proliferation in a spatially-restricted manner via a soluble factor when co-cultured in microfluidic chambers. Comparative spatial transcriptomic analysis of the cranial sutures in vivo confirmed a positive association between sensory axons and proliferative MPCs. SpatialTime analysis across the developing suture revealed regional-specific alterations in BMP and TGFÎ² signaling pathway transcripts in response to TrkA inhibition. RNA sequencing of DRG cell bodies following direct axonal co-culture with MPCs confirmed alterations in BMP/TGFÎ² signaling pathway transcripts. Among these, the BMP inhibitor FSTL1 (Follistatin-like 1) replicated key features of the neural-to-bone influence, including mitogenic and anti-osteogenic effects via inhibition of BMP/TGFÎ² signaling. Taken together, our results demonstrate that sensory nerve-derived signals, including FSTL1, function to coordinate cranial bone patterning by regulating MPC proliferation and differentiation in the suture mesenchyme.

overall_design:
  P0 calvaria were isolated from TrkAF592A homozygous (mutant) and heterozygous (control) mice in which mothers were treated with 1NMPP1 via their drinking water from the time of conception through birth. Sagittal sutures and flanking parietal bones were dissected out, stacked and fresh frozen in OCT. Frozen sections were applied to the 10x Visium spatial transcriptomics gene expression platform and processed according to manufacturers protocols. Following sequencing, alignment and image registration was conducted using SpaceRanger.

citation:
  Tower, Robert J et al. “Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling.” Proceedings of the National Academy of Sciences of the United States of America vol. 118,42 (2021): e2103087118. doi:10.1073/pnas.2103087118


dataset_id: STDS0000110
species: Mus musculus
tissues: Heart
technologies: 10x Visium
disease: Heart regeneration and repair
submission_date: 2020-12-21 00:00:00
last_modified: 2021-09-27 00:00:00
contributors: Miao Cui;Ning Liu;Rhonda Bassel-Duby;Eric N Olson
contacts: miaocui713@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163629
platforms: GPL19057
pmid: 34489413
title:
  Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance [Spatial transcriptome]

summary:
  Heart disease can be caused by ischemic coronary artery injury, hypertension, and chemotherapy, all of which lead to loss or dysfunction of cardiac muscle. The adult mammalian heart lacks the ability to regenerate. In contrast, the heart of neonatal mice, within the first week after birth, possesses a unique ability to regenerate lost myocardium following injury, mediated by proliferation of cardiomyocytes. The mechanisms whereby neonatal cardiomyocytes adapt to injury-induced stress conditions and activate regenerative cellular programs remain to be defined. Here, we show that Nrf1, an endoplasmic reticulum (ER) bound transcription factor, is expressed in regenerating cardiomyocytes. Genetic deletion of Nrf1 prevented cardiomyocytes from activating a transcriptional program required for heart regeneration, revealed by single-nucleus RNA sequencing (snRNA-seq).  Conversely, adeno-associated virial (AAV) overexpression of Nrf1 protected the adult mouse heart from ischemia/reperfusion (I/R) injury.  Nrf1 also protected human induced pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) from doxorubicin-induced cardiotoxicity. The protective function of Nrf1 is mediated by a dual stress response mechanism involving activation of the proteasome and redox balance. Our findings reveal a mechanistic interplay between adaptive stress responses and heart regeneration, and highlight the central role of Nrf1 in these processes.

overall_design:
  Exmination of transcriptome changes in neonatal rat ventricular cardiomyocytes overexpresing Nrf1 or Nrf2 .

citation:
  Cui, Miao et al. “Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance.” Nature communications vol. 12,1 5270. 6 Sep. 2021, doi:10.1038/s41467-021-25653-w


dataset_id: STDS0000086
title: Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface
species: Danio rerio
tissues: Skin
technologies: 10x Visium
disease: Cancer
submission_date: 2020-10-20 00:00:00
last_modified: 2021-09-23 00:00:00
contributors: Reuben Moncada;Miranda V Hunter
contacts: hunterm@mskcc.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159709
platforms: GPL20828;GPL24995
pmid: 34725363
has_paired: STDS0000086
summary:
  Cancer cells interact with a wide variety of other cell types, but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single-cell RNA-seq (scRNA-seq) has helped define these TME cell types, it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here, we integrate spatial transcriptomics with scRNA-seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well-defined transgenic zebrafish model of BRAFV600E-driven melanoma, we identify a transcriptionally unique â€œinterfaceâ€ cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased, data-driven approach, we identify spatially-patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA-seq, we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes, and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress their expression outside of this region. This unique ETS-driven interface transcriptional state is conserved across ten different human patient samples, suggesting this is a conserved feature of human melanoma. Taken together, our results demonstrate the power of spatial and single-cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues.Â 

overall_design:
  Spatial transcriptomics (Visium platform) of zebrafish bearing BRAF-V600E driven melanomas. Single-cell RNA-seq (10x Genomics v3) of two such zebrafish. Single-nucleus RNA-seq (10x Genomics v3) of three such zebrafish (pooled into one reaction).

citation:
  Hunter, Miranda V et al. “Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface.” Nature communications vol. 12,1 6278. 1 Nov. 2021, doi:10.1038/s41467-021-26614-z


dataset_id: STDS0000057
title: ZESTA: Zebrafish Embryogenesis Spatiotemporal Transcriptomic Atlas
species: Danio rerio
tissues: Embryo
technologies: Stereo-Seq
disease: Embryo development
submission_date: 2021-09-16 00:00:00
last_modified: 2021-09-16 00:00:00
platforms: DNBSEQ-T1
pmid: 35512701
has_paired: STDS0000057
summary:
  Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 152,977 spots at a resolution of 10x10x15 µm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

citation:
  Liu, Chang et al. “Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis.” Developmental cell vol. 57,10 (2022): 1284-1298.e5. doi:10.1016/j.devcel.2022.04.009

accessions:
  https://db.cngb.org/search/project/CNP0002220/;https://stereomap.cngb.org/zebrafish/image_staining;https://stereomap.cngb.org/zebrafish/data_index;https://db.cngb.org/stomics/zesta/


dataset_id: STDS0000088
title: Neuroinflammatory astrocyte subtypes in the mouse brain [Visium]
species: Mus musculus
tissues: Brain
organ_parts: Coronal brain
development_stages: P30-P35
technologies: 10x Visium
disease: Brain cortex
summary: Spatial transcriptomics of saline- and LPS-injected Aldh1l1egfp mice 24 h after injection
submission_date: 2021-01-19 00:00:00
last_modified: 2021-09-02 00:00:00
contributors: Philip Hasel;Shane Liddelow
contacts: philip.hasel@nyulangone.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165098
platforms: GPL24247
pmid: 34413515
overall_design:
  Brains from 3 saline- and 3 LPS-injected female mice were sectioned to 10 um and used for Visium Spatial Transcriptomics

citation:
  Hasel, Philip et al. “Neuroinflammatory astrocyte subtypes in the mouse brain.” Nature neuroscience vol. 24,10 (2021): 1475-1487. doi:10.1038/s41593-021-00905-6


dataset_id: STDS0000067
species: Homo sapiens
tissues: Bladder
organ_parts: Muscle-invasive bladder cancer
technologies: 10x Visium
disease: Bladder cancer
submission_date: 2021-04-01 00:00:00
last_modified: 2021-08-24 00:00:00
contributors: Kenneth H Gouin III;Nathan Ing;Simon R Knott;Dan Theodorescu
contacts: Kgouiniii@gmail.com
platforms: Illumina NovaSeq 6000
pmid: 34385456
has_paired: STDS0000067
title:
  A new epithelial cell subpopulation predicts response to surgery, chemotherapy, and immunotherapy in bladder cancer

summary:
  The advent of neoadjuvant chemotherapy (NAC) prior to surgery and immune checkpoint therapy (ICT) have revolutionized bladder cancer management1-7. However, stratification of patients that would benefit most from these modalities remains a major clinical challenge. Here, we combine single nuclei RNA sequencing with spatial transcriptomics and single cell resolution spatial proteomic analysis of human bladder cancer to identify a novel epithelial subpopulation with therapeutic response prediction ability. These cells were defined by expression of Cadherin 12 (CDH12, N-Cadherin 2), catenins and other epithelial markers. CDH12-enriched tumors define patients with poor outcome following surgery with or without NAC. In contrast, CDH12-enriched tumors had a superior response to ICT. In all settings, patient stratification by tumor CDH12 enrichment offered better prediction of outcome than currently established bladder cancer subtypes. Molecularly, the CDH12 population resembles an undifferentiated state with inherent chemoresistance mediated through ALDH1A1 expression and fibroblast activation potential. Furthermore, CDH12-enriched cells express PD-L1 and PD-L2 and co-localize with exhausted T-cells, possibly mediated through CD49a (ITGA1), providing one explanation for ICT efficacy in these tumors. Altogether, this study describes a new cancer cell population with an intriguing diametric response to the major therapeutic modalities in bladder cancer. Importantly, it also provides a compelling rationale for the design of novel biomarker guided therapeutic clinical trials.

overall_design:
  Visium spatial transcriptomics of human treatment-na茂ve muscle-invasive bladder cancer (n=4) fresh-frozen tissue.

citation:
  Gouin, Kenneth H 3rd et al. “An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer.” Nature communications vol. 12,1 4906. 12 Aug. 2021, doi:10.1038/s41467-021-25103-7

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171351;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169379


dataset_id: STDS0000052
title: Adult Mouse Brain (FFPE)
species: Mus musculus
tissues: Brain
development_stages: >8 weeks
sex: Male
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2021-08-16 00:00:00
last_modified: 2021-08-16 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.3.0/Visium_FFPE_Mouse_Brain
has_paired: SCDS0000016
summary:
  5µm section from Mus musculus brain. FFPE tissue purchased from Adlego and embedded by BioIVT.

  Sex: Male
  Age: >8 weeks
  Strain: C57BL/6
  Section Orientation: Coronal
  Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A). Sequenced on an Illumina NovaSeq with approximately 28,826 reads per spot with dualindex set SITSB7, 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 120bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode. 2,264 spots detected under tissue.


dataset_id: STDS0000106
title: Spatial transcriptomic reference of the endometrium and myometrium of women in reproductive age
species: Homo sapiens
tissues: Uterus
development_stages: Adult;35-year-old to 39-year-old;21-year-old to 25-year-old
sex: Female
technologies: 10x Visium
disease: Normal atlas
overall_design: menstrual cycle stage
submission_date: 2021-08-11 00:00:00
last_modified: 2021-08-11 00:00:00
contributors: Luz Garcia-Alonso
contacts: lg18@sanger.ac.uk
accessions: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9260/
pmid: 34857954
summary:
  Human uterine samples were analysed using Visium technology (10X Genomics) to generate a cellular 2D map of the endometrium to study its temporal and spatial changes across the menstrual cycle. Dataset comprises 4 samples from two women in their reproductive age.

citation:
  Garcia-Alonso, Luz et al. “Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.” Nature genetics vol. 53,12 (2021): 1698-1711. doi:10.1038/s41588-021-00972-2


dataset_id: STDS0000092
title: Spatial transcriptomics of human brain metastases
species: Homo sapiens
tissues: Brain
technologies: 10x Visium
disease: Brain metastases cancer
summary: Spatial transcriptomics of six surgically-resected human brain metastasis samples
submission_date: 2021-07-06 00:00:00
last_modified: 2021-08-06 00:00:00
contributors: William H Hudson
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179572
platforms: GPL24676
pmid: 35707680
overall_design:
  After surgical resection, parts of six human brain metastases were embedded in OCT and frozen in a dry ice/2-methylbutane bath. 10 脦录M sections were placed on Visium gene expression slides which were stored at -80C until use. Slides were methanol fixed and stained with H&E and imaged at 10x on a Biotek Lionheart microscope. Tissues were permeabilized and libraries generated according to the manufacturer's protocols. Images for all samples are available in all_spatial_images.tar.gz.

citation:
  Hudson, William H, and Lisa J Sudmeier. “Localization of T cell clonotypes using the Visium spatial transcriptomics platform.” STAR protocols vol. 3,2 101391. 10 Jun. 2022, doi:10.1016/j.xpro.2022.101391


dataset_id: STDS0000100
title: Comparison of spatial sequencing in leprosy lesions from lepromatous and reversal reaction patients
species: Homo sapiens
tissues: Skin
technologies: 10x Visium
disease: Lepromatous
overall_design: Examine differences between Lepromatous and Reversal reaction lesions by spatial sequencing
submission_date: 2021-02-28 00:00:00
last_modified: 2021-08-03 00:00:00
contributors: Feiyang Ma;Olesya Plazyo;Johann E Gudjonsson;Matteo Pellegrini;Robert L Modlin
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167889
platforms: GPL24676
pmid: 34168371
summary:
  Granulomas are complex cellular structures comprised predominantly of macrophages and lymphocytes that function to contain and kill invading pathogens. Here, we investigated single cell phenotypes associated with antimicrobial responses in human leprosy granulomas by applying single cell and spatial sequencing to leprosy biopsy specimens. We focused on reversal reactions (RR), a dynamic process in which some patients with disseminated lepromatous leprosy (L-lep) transition towards self-limiting tuberculoid leprosy (T-lep), mounting effective antimicrobial responses. We identified a set of genes encoding proteins involved in antimicrobial responses that are differentially expressed in RR versus L-lep lesions, and regulated by IFN- and IL-1. By integrating the spatial coordinates of the key cell types and antimicrobial gene expression in RR and T-lep lesions, we constructed a map revealing the organized architecture of granulomas depicting compositional and functional layers by which macrophages, T cells, keratinocytes and fibroblasts contribute to the antimicrobial response.

citation:
  Ma, Feiyang et al. “The cellular architecture of the antimicrobial response network in human leprosy granulomas.” Nature immunology vol. 22,7 (2021): 839-850. doi:10.1038/s41590-021-00956-8


dataset_id: STDS0000056
title: ARTISTA: Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas
species: Ambystoma mexicanum
tissues: Brain
technologies: Stereo-Seq
disease: Injured brain
submission_date: 2021-08-01 00:00:00
last_modified: 2021-08-01 00:00:00
accessions: https://db.cngb.org/search/project/CNP0002068/;https://db.cngb.org/stomics/artista/
platforms: DNBSEQ-T1
pmid: 36048929
development_stages:
  Developmental stage 44;Developmental stage 54;Developmental stage 57;Juvenile;Adult;Metamorphosed animals;2 days post injury;5 days post injury;10 days post injury;15 days post injury;20 days post injury;30 days post injury;60 days post injury

summary:
  Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas (ARTISTA) is a spatially resolved transcriptomic data resource that provides visualization of gene expression across the regeneration and development stages of axolotl telencephalon at single cell resolution, aiming to provide a systematic dissection of the molecular events underlying neural regeneration in the axolotl brain, laying the foundation for further mechanistic studies. To comprehensively understand cellular dynamics occurred during axolotl brain regeneration and development, here, we carried out a series of spatial transcriptome analyses on serial sections along the rostral-caudal axis of 2 (3 sections), 5 (3 sections), 10 (3 sections), 15 (4 sections), 20 (3 sections), 30 and 60 days post injury (DPI) brain tissues after removal of a reproducible portion of dorsal pallium in left telencephalic hemisphere of 11 cm length axolotl. We also collected sections from developmental (stage 44, 54, and 57), juvenile, adult, and metamorphosed axolotl telencephalons. Based on this dataset, researchers can quickly explore the gene expression profiles of their interested cell types in spatial map across different regeneration and development stages of axolotl telencephalon.

citation:
  Wei, Xiaoyu et al. “Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration.” Science (New York, N.Y.) vol. 377,6610 (2022): eabp9444. doi:10.1126/science.abp9444


dataset_id: STDS0000069
title: High-depth spatial transcriptome analysis by photo-isolation chemistry
species: Homo sapiens;Mus musculus
tissues: Cell line
organ_parts: HeLa cells;NIH3T3 cells;Neural tube
development_stages: E14.5
sex: Male
technologies: PIC-seq
disease: Normal atlas
submission_date: 2020-01-10 00:00:00
last_modified: 2021-07-28 00:00:00
contacts: oki.shinya.3w@kyoto-u.ac.jp
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143413
platforms: Illumina HiSeq 1500
pmid: 34285220
summary:
  We established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest.

overall_design:
  We performed PIC to isolate expression profiles from small domain of the E14.5 mouse neural tube. We performed PIC to isolate expression profiles from small domain of HeLa cells or NIH3T3 cells. We performed PIC to isolate expression profiles from each of the major hippocmpal [CA1, CA2 and dentate gyrus (DG) ] in 8 weeks male mice.

contributors:
  Mizuki Honda;Shinya Oki;Ryuichi Kimura;Akihito Harada;Kazumitsu Maehara;Kaori Tanaka;Chikara Meno;Yasuyuki Ohkawa

citation:
  Honda, Mizuki et al. “High-depth spatial transcriptome analysis by photo-isolation chemistry.” Nature communications vol. 12,1 4416. 20 Jul. 2021, doi:10.1038/s41467-021-24691-8


dataset_id: STDS0000095
title: Spatiotemporal role of the lncRNA Evx1as in embryonic patterning
species: Mus musculus
development_stages: Embryonic 7 days
technologies: Geo-seq
disease: Embryo development
submission_date: 2017-09-26 00:00:00
last_modified: 2021-07-25 00:00:00
contributors: Luo S;Peng G;Cui G;Lu J;Jing N;Shen X
contacts: bioyuyang@hotmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104292
platforms: GPL17021
pmid: 29420831
cell_types:
  embryonic stem cells;4x polyA KI in embryonic stem cells;Evx1as+/- proximal posterier;Evx1as+/- distal posterier;Evx1as-/- proximal posterier;Evx1as-/- distal posterier;Evx1as+/- Primtive streak layer;Evx1as+/- mesoderm layer;Evx1as+/- anterior epiblast cells;Evx1as-/- Primtive streak layer;Evx1as-/- mesoderm layer;Evx1as-/- anterior epiblast cells

summary:
  We performed spatial transcriptome analysis on cryosections of gastrulating embryos from E6.5 to E7.5 by low-input RNA sequencing (Geo-seq). Careful spatial transcriptomic analysis revealed that the lncRNA Evx1as plays a transient spatiotemporal role in regulating embryonic patterning during gastrulation, yet is dispensable for overall development and survival. Altogether, these results suggest that many lncRNAs are generally dispensable for normal development and survival, but may be selectively required in a particular context in vivo.

overall_design:
  All RNA-seq(s) were designed to reveal the spatiotemporal role of lncRNA Evx1as in embryonic patterning.

citation:
  Han, Xue et al. “Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development.” Journal of molecular cell biology vol. 10,2 (2018): 175-178. doi:10.1093/jmcb/mjy003


dataset_id: STDS0000047
title: Human Prostate Cancer, Adjacent Normal Section with IF staining (FFPE)
species: Homo sapiens
tissues: Prostate
sex: Male
technologies: 10x Visium
disease: Prostate Cancer
submission_date: 2021-07-21 00:00:00
last_modified: 2021-07-21 00:00:00
has_paired: SCDS0000005
summary:
  10µm section from Adenocarcinoma of Homo sapiens Prostate. FFPE tissue purchased from Indivumed Homo sapiens Tissue Specimens (Indivumed). Original diagnosis with adenocarcinoma.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.3.0/Visium_FFPE_Human_Prostate_IF


dataset_id: STDS0000101
species: Mus musculus
tissues: Colon;Liver
organ_parts: Colon;Liver
development_stages: 8 weeks
technologies: Seq-Scope
disease: Normal atlas
submission_date: 2021-03-26 00:00:00
last_modified: 2021-07-19 00:00:00
contacts: leeju@umich.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706
platforms: GPL17769;GPL21103;GPL21273
pmid: 34115981
title:
  Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels

summary:
  Purpose: we propose Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale.|Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array.    Computational Methods: Tissue boundaries are detected by using a custom python code to draw a smoothed density plot to visualize the density of HiSeq reads in a given XY space of each tile. Digital gene expression (DGE) matrices are  generate using STAR/STARsolo 2.7.5c with Gene,GeneFull, Velocyto, and polyAtrimming options.  Data binning is performed by dividing the imaging space into 100 μm2 square grid with 10 μm simple side or 25 μm2 square grid with 5 μm side and collapsing all HDMI-UMI information into one barcode. Binned DGE matrix was analyzed in the Seurat v4 package for clustering analysis.

overall_design:
  A total of 2 Seq-Scope experiments (colon and liver) were run. Livers were collected from 8 week-old control (Depdc5F/F/Tsc1F/F, male) and TD (Alb-Cre/Depdc5F/F/Tsc1F/F, female) mice. Colons are from 8-week-old C57BL/6 wild-type male mice.

contributors:
  Chun-Seok Cho;Jingyue Xi;Yichen Si;Jun H Lee;Hyun M Kang;Sung-Rye Park;Jer-En Hsu;Myungjin Kim;Goo Jun

citation:
  Cho, Chun-Seok et al. “Microscopic examination of spatial transcriptome using Seq-Scope.” Cell vol. 184,13 (2021): 3559-3572.e22. doi:10.1016/j.cell.2021.05.010


dataset_id: STDS0000076
title: Spatio-temporal mRNA tracking in the early zebrafish embryo
species: Danio rerio;Xenopus laevis;Xenopus tropicalis
tissues: Embryo
organ_parts: Embryo
technologies: Tomo-seq
disease: Embryo development
submission_date: 2020-09-30 00:00:00
last_modified: 2021-07-15 00:00:00
contacts: JanPhilipp.Junker@mdc-berlin.de
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158849
platforms: GPL20828;GPL21248;GPL21741;GPL24884
pmid: 34099733
summary:
  We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.

overall_design:
  Spatial transcriptomic data (tomo-seq) from zebrafish one-cell stage embroys, mature X. laevis and X. tropicalis oocytes. Single-cell metabolic labeling (scSLAM-seq) of zebrafish embryos at 6 hpf.

contributors:
  Karoline Holler;Anika Neuschulz;Philipp Boß;Janita Mintcheva;Roberto Arsiè;Uwe Ohler;Markus Landthaler;Jan P Junker

citation:
  Holler, Karoline et al. “Spatio-temporal mRNA tracking in the early zebrafish embryo.” Nature communications vol. 12,1 3358. 7 Jun. 2021, doi:10.1038/s41467-021-23834-1


dataset_id: STDS0000010
species: Sus scrofa
tissues: Muscle
organ_parts: Representative psoas major muscle
sex: Female
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-11-20 00:00:00
last_modified: 2021-07-08 00:00:00
contributors: Zeng B;Jin L
contacts: 14044@sicau.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161882
platforms: Illumina NovaSeq 6000
pmid: 34140474
title:
  A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

cell_types:
  type I myofibers of the psoas major (PM) muscle;type IIA myofibers of the psoas major (PM) muscle;type  IIB myofibers of the psoas major (PM) muscle

summary:
  Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.

overall_design:
   This study takes pig psoas major muscle tissue in two replicates as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were inentified.

citation:
  Jin, Long et al. “A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription.” Nature communications vol. 12,1 3715. 17 Jun. 2021, doi:10.1038/s41467-021-23560-8


dataset_id: STDS0000080
title: Sci-Space E14 Mouse Embryo Data
species: Mus musculus
tissues: Embryo
technologies: sci-Space
disease: Embryo development
submission_date: 2021-02-12 00:00:00
last_modified: 2021-07-01 00:00:00
contributors: Sanjay R Srivatsan;Mary Regier
contacts: sanjays@uw.edu, sanjayrsrivatsan@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166692
platforms: GPL21626
pmid: 34210887
has_paired: STDS0000080
summary:
  Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.

overall_design:
  Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.

citation:
  Srivatsan, Sanjay R et al. “Embryo-scale, single-cell spatial transcriptomics.” Science (New York, N.Y.) vol. 373,6550 (2021): 111-117. doi:10.1126/science.abb9536


dataset_id: STDS0000011
title: Vitamin D sufficiency enhances differentiation of patient-derived prostate epithelial organoids
species: Homo sapiens
tissues: Prostate
organ_parts: Prostate epithelial organoids
cell_types: stem cell;dividing cells;The “IntegrinHigh”;progenitor;luminal
technologies: 10x Visium;scRNA
disease: Normal atlas
overall_design: Two samples:ETOH, 25D
submission_date: 2020-10-20 00:00:00
last_modified: 2021-06-19 00:00:00
contributors: Garcia J;Loitz C;Nonn L
contacts: lnonn@uic.edu
platforms: Illumina NovaSeq 6000
pmid: 33458620
has_paired: STDS0000011
summary:
  Spatially resolved gene expression was prepard by dissociated hman prostate tissue to single cells, and collected & prepped for RNA-seq using the Visium Spatial Gene Expression kit. 5000 cells were collected and sequenced at a depth of 50k cells/gene on a 2X150nt lane in a NovaSeq 6000. SpaceRanger alignment was performed to produce the RAW files

citation:
  McCray, Tara et al. “Vitamin D sufficiency enhances differentiation of patient-derived prostate epithelial organoids.” iScience vol. 24,1 101974. 5 Jan. 2021, doi:10.1016/j.isci.2020.101974

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159697;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142489


dataset_id: STDS0000094
title: Clump sequencing exposes the spatial expression programs of intestinal secretory cells
species: Mus musculus
development_stages: 3 months;4 months
technologies: ClumpSeq
disease: Normal atlas
submission_date: 2020-07-20 00:00:00
last_modified: 2021-06-15 00:00:00
contributors: Rita Manco;Inna Averbukh;Keren B Halpern;Porat Ziv;Ido Amit;Shalev Itzkovitz
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154714
platforms: GPL21626
pmid: 34031373
summary:
  We molecularly characterized Clumps and single cells from Jejunum. This enable us to uncover the zonation of rare secretory cells on crypt to villus axis.

overall_design:
  mRNA profiles from clumps and single cells, EDTA isolated jejunum epithelial clumps and single cells were sequenced in several batches in an Illumina NextSeq.

citation:
  Manco, Rita et al. “Clump sequencing exposes the spatial expression programs of intestinal secretory cells.” Nature communications vol. 12,1 3074. 24 May. 2021, doi:10.1038/s41467-021-23245-2


dataset_id: STDS0000013
species: Mus musculus
tissues: Cerebella
cell_types: Cerebellar granule neuron progenitors
technologies: Spatial Transcriptomics;scRNA
disease: Cerebella development
submission_date: 2020-08-21 00:00:00
last_modified: 2021-06-14 00:00:00
contributors: Wang J;Gao W
contacts: wj860520@163.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156633
platforms: Illumina NovaSeq 6000
pmid: 34210306
title:
  Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

summary:
  The progenitor/differentiation states of cerebellum granule cells have been investigated for many years. Deregulation of granule cells development is associated with the pathogenesis of medulloblastoma (MB).Our study reveals the cellular and spatial organization of cerebellar granule cells and provide direct evidence showing the similarity and discrepancy between normal development and tumorigenesis

overall_design:
  Single cell mRNA profiles of 2 samples from Math1-GFP mice, 2 samples from Dcx-DsRed mice, 2 samples from WT mice and 3 SHH MBs from Patched+/- mice were generated by 10x Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina). Spatial transcriptomics (ST) profiles of 2 samples of P7 WT mice were generated by 10x Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina).

citation:
  Luo, Wenqin et al. “Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma.” BMC biology vol. 19,1 135. 1 Jul. 2021, doi:10.1186/s12915-021-01071-8


dataset_id: STDS0000049
title: Human Breast Cancer: Ductal Carcinoma In Situ, Invasive Carcinoma (FFPE)
species: Homo sapiens
tissues: Breast
sex: Female
technologies: 10x Visium
disease: Breast Cancer
submission_date: 2021-06-09 00:00:00
last_modified: 2021-06-09 00:00:00
has_paired: SCDS0000018
summary:
  5 µm section from Invasive Ductal Carcinoma of Homo sapiens Breast. FFPE tissue purchased from BioIVT Asterand Homo sapiens Tissue Specimens (BioIVT):

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.3.0/Visium_FFPE_Human_Breast_Cancer


dataset_id: STDS0000048
title: Normal Human Prostate (FFPE)
species: Homo sapiens
tissues: Prostate
sex: Male
technologies: 10x Visium
disease: Normal atlas
submission_date: 2021-06-09 00:00:00
last_modified: 2021-06-09 00:00:00
has_paired: SCDS0000017
summary:
  5 µm section from Homo sapiens prostate. FFPE tissue purchased from Indivumed Homo sapiens Tissue Specimens (Indivumed).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.3.0/Visium_FFPE_Human_Normal_Prostate


dataset_id: STDS0000046
title: Human Prostate Cancer, Adenocarcinoma with Invasive Carcinoma (FFPE)
species: Homo sapiens
tissues: Prostate
sex: Male
technologies: 10x Visium
disease: Prostate Cancer
submission_date: 2021-06-09 00:00:00
last_modified: 2021-06-09 00:00:00
has_paired: SCDS0000017
summary:
  5 µm section from Adenocarcinoma of Homo sapiens Prostate. FFPE tissue purchased from Indivumed Homo sapiens Tissue Specimens (Indivumed).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.3.0/Visium_FFPE_Human_Prostate_Cancer


dataset_id: STDS0000009
species: Homo sapiens
tissues: Embryo
organ_parts: Liver
development_stages: 8 PCW;17 PCW
technologies: 10x Visium
disease: Liver development
overall_design: The sample contained one 8-postconception weeks and one 17-postconception weeks fetal livers.
submission_date: 2020-02-19 00:00:00
last_modified: 2021-06-09 00:00:00
contributors: Hou X;Dai Y
contacts: houxl115@126.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167096
platforms: Illumina NovaSeq 6000
pmid: 34095116
title:
  Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver

cell_types:
  B cell;dendritic cell (DC);DC1;DC2;early erythroblast;endothelial;HSC_MPP;fibroblast;hepatocyte;kupffer;ILC;late erythroblast;MEMP;mast cell;megakaryocyte;mid erythroblast;monocyte;monomac;neutrophilmyeloid;NK;pDC;Pre;PreB;ProB;VCAM1+

summary:
  We use single-cell RNA-seq technology for unbiased analysis of fetal livers over developmental time from 8 postconception weeks (PCW) and 17 PCW in humans.

citation:
  Hou, Xianliang et al. “Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver.” Frontiers in cell and developmental biology vol. 9 652408. 20 May. 2021, doi:10.3389/fcell.2021.652408


dataset_id: STDS0000007
species: Mus musculus;Homo sapiens
tissues: Kidney
development_stages: 59-year-old;8-10 weeks
sex: Male
technologies: 10x Visium;scRNA
disease: Murine ischemia | Reperfusion injury (IRI) and cecal ligation puncture (CLP) models of AKI
submission_date: 2020-04-02 00:00:00
last_modified: 2021-06-05 00:00:00
contributors: Eadon Michael;Ricardo Melo Ferreira;Ying-Hua Cheng
platforms: Illumina NovaSeq 6000
pmid: 34003797
has_paired: SCDS0000041
title:
  Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury

summary:
   Single cell sequencing studies have characterized the transcriptomic signature of cell types within the kidney. However, the spatial distribution of acute kidney injury (AKI) is regional and affects cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy. The predicted cell type spots corresponded with the underlying histopathology. To study the implications of AKI on transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were associated with injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. Neutrophils infiltrated the renal medulla in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubules. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing complements single cell sequencing by uncovering mechanisms driving immune cell infiltration and detection of relevant cell subpopulations.

overall_design:
  A single human reference nephrectomy (female aged 59 without histologic evidence of kidney disease) was acquired from the Biopsy Biobank Cohort of Indiana (BBCI). From age-matched 8-10 week old 129/ SvEv mice (Taconic Biosciences, Albany, New York), tissues were acquired from a sham mouse in which the abdomen was opened and sutured back and mice which underwent ischemia-reperfusion injury (IRI) or cecal ligation and puncture (CLP). In the IRI model both renal pedicles were exposed and clamped for 22 minutes through a midline incision then released. In the CLP model, the cecum was ligated and punctured with a 25 gauge needle. Kidneys were excised upon sacrifice 6 hours after each procedure and frozen in Optimal Cutting Temperature (OCT) compound. Slide preparation (CG000240_Demonstrated_Protocol_VisiumSpatialProtocols_TissuePreparationGuide_Rev_A, 10x Genomics), imaging (CG000241_VisiumImagingGuidelinesTN_Rev_A, 10x Genomics), mRNA extraction, library preparation, and sequencing (CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10x Genomics) were conducted according to Visium Spatial Gene Expression protocols . Frozen transverse 10 碌m sections from the human nephrectomy or each murine model were placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Tissue sections were fixed in methanol and stained with hematoxylin and eosin (H&E). Stained tissue sections were permeabilized for 12 minutes, and the cDNA libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 28bp+120bp paired-end sequencing mode.

citation:
  Melo Ferreira, Ricardo et al. “Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury.” JCI insight vol. 6,12 e147703. 22 Jun. 2021, doi:10.1172/jci.insight.147703

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171406;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171639


dataset_id: STDS0000096
species: Homo sapiens
tissues: Heart
organ_parts: IPS cells;Transmural cross-section of the heart
development_stages: Adult
technologies: Tomo-seq
disease: Heart failure
submission_date: 2018-05-22 00:00:00
last_modified: 2021-05-24 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114770
platforms: GPL18573
pmid: 35576477
title:
  Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in cardiomyopathy

summary:
  Aims | Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive fibro-fatty replacement of the myocardium, arrhythmias, and sudden death. While myocardial degeneration and fibro-fatty replacement occurs in specific locations, the underlying molecular changes remain poorly characterized. Here we aim to delineate local changes in gene expression to help identify new genes or pathways that are relevant for specific remodelling processes occurring during ACM. | Methods and Results | Using Tomo-Seq, a genome-wide transcriptional profiling with high spatial resolution, we created a transmural epicardial to endocardial gene expression atlas of an explanted ACM heart to gain molecular insights into disease-driving processes. This enabled us to link gene expression profiles to the different regional remodelling responses and allowed us to identify genes that are potentially relevant for disease progression. In doing we revealed BTB (broad-complex, tramtrack, bric-Ã -brac) domain containing 11 (ZBTB11) to be specifically enriched at sites of active fibrofatty replacement of myocardium. Immunohistochemistry indicated ZBTB11 to be enriched in cardiomyocytes flanking fibrofatty areas, which could be confirmed in multiple cardiomyopathy patients. Forced overexpression of ZBTB11 in iPS-derived cardiomyocytes showed ZBTB11 to function as a potent inducer of cardiomyocyte atrophy. | Conclusion | By combining spatial transcriptomics with classical histological approaches we identified gene expression changes underlying local remodelling responses in ACM. In doing so we found ZBTB11 to function as a relevant driver of cardiomyocyte atrophy. These data show the power of Tomo-Seq to unveil new molecular mechanisms and indicate ZBTB11 as a potential new target for cardiomyopathy. 

overall_design:
  The dataset contains the following experiments: 1. Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections on diseased heart. After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113). Libraries were sequenced on Illumina NextSeq 500 using 75p paired end sequencing. 2. Bulk RNA-seq processed by the CEL-seq protocol. IPS derived cardiomyocytes were transduced with AAV-ZBTB11, AAV-GFP, or not transduced. 7 days after transduction, cells were harvested and RNA-Seq was performed. RNA-Seq on nontransduced control, AAV-GFP transduced and AAV-ZBTB11 transduced iPS derived cardiomyocytes.

contributors:
  Grégory Lacraz;Ábel Vértesy;Cornelis J. Boogerd;Ilaria Perini;Hesther de Ruiter;Andreas Brodehl;Petra van der Kraak;Mauro Giacca;Manon Huibers;Nicolaas de Jonge;Jan Philip Junker;Aryan Vink;Eva van Rooij

citation:
  Boogerd, Cornelis J et al. “Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.” Cardiovascular research vol. 119,2 (2023): 477-491. doi:10.1093/cvr/cvac072


dataset_id: STDS0000006
title: A coordinated progression of progenitor cell states initiates urinary tract development
species: Mus musculus
tissues: Embryo
organ_parts: Trunk
technologies: 10x Visium;scRNA
disease: E9.5 Pax2GFP Mus musculus embryos
overall_design: Identify cell heterogenity and state transitions in the developing urinary tract
submission_date: 2020-10-26 00:00:00
last_modified: 2021-05-18 00:00:00
contributors: SanchezFerras O;Pacis A;Sotiropoulou M;Zhang Y;Wang YC;Bourgey M;Bourque G;Ragoussis I;Bouchard M
contacts: alain.pacis@mcgill.ca
platforms: Illumina NovaSeq 6000
pmid: 33976190
summary:
  To study cell heterogeneity and state transitions in the developing urinary tract we performed spatial transcriptomics from the trunk of E9.5 Pax2GFP mouse embryos using the 10x Genomics Visium Spatial Gene Expression protocol

citation:
  Sanchez-Ferras, Oraly et al. “A coordinated progression of progenitor cell states initiates urinary tract development.” Nature communications vol. 12,1 2627. 11 May. 2021, doi:10.1038/s41467-021-22931-5


dataset_id: STDS0000133
species: Homo sapiens;Mus musculus
tissues: Liver
cell_types: mouse cell line:3T3;human cell line:HEK293T
technologies: XYZeq
disease: Liver cancer
submission_date: 2021-01-07 00:00:00
last_modified: 2021-05-12 00:00:00
contributors: Y Lee;D Bogdanoff;Y Wang;G Hartoularos;A Marson;E D Chow;C J Ye
contacts: george.hartoularos@ucsf.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164430
platforms: GPL21103
pmid: 33883145
title:
  Spatially resolved single-cell RNA-sequencing reveals expression heterogeneity in tumor microenvironment

summary:
  To better understand how individual cells function within an anatomical space, we developed XYZeq, a novel scRNA-seq workflow that uses combinatorial indexing in microwells to encode spatial metadata into scRNA-seq libraries. We used XYZeq to profile heterotopic mouse liver and spleen tumor models to capture transcriptomes from tens of thousands of cells across a total of eight tissue slices.

overall_design:
  Spatially resolved single-cell RNA-sequencing from eight tissue sections of MC38-injected liver and spleen organs (samples L30C and L30C8 are from the same slice). Additional experiments using cell lines and comparing to droplet-based single-cell RNA-seq.

citation:
  Lee, Youjin et al. “XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.” Science advances vol. 7,17 eabg4755. 21 Apr. 2021, doi:10.1126/sciadv.abg4755


dataset_id: STDS0000028
title: Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody
species: Homo sapiens
tissues: Breast
development_stages: >50 days
technologies: 10x Visium
disease: Invasive Ductal carcinoma
submission_date: 2021-05-11 00:00:00
last_modified: 2021-05-11 00:00:00
has_paired: SCDS0000018
summary:
  Visium Spatial Gene Expression Dataset processed with Spaceranger 1.2. Invasive ductal carcinoma was obtained from BioIVT: ASTERAND (Westbury, NY). Raw sequencing data (FASTQ and BAM files) are not included. This dataset is published in Nature Biotechnology: Spatial transcriptomics at subspot resolution with BayesSpace.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/V1_Human_Invasive_Ductal_Carcinoma


dataset_id: STDS0000090
species: Mus musculus
cell_types: mixed -whole tissue
development_stages: 8 weeks;6 weeks
sex: Female
technologies: 10x Visium
disease: Cancer
submission_date: 2021-05-03 00:00:00
last_modified: 2021-05-07 00:00:00
contacts: ido.amit@weizmann.ac.il
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173776
platforms: GPL24247
pmid: 35449415
title:
  Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (Spatial scRNA-Seq)

summary:
  The function of mammalian cells is largely influenced by their tissue microenvironment and by inter- celllular interactions. Advances in spatial transcriptomics open the way for studying these important determinants of cellular function, by enabling a transcriptome wide evaluation of gene expression in-situ. A critical limitation of the current technologies, however, is that their resolution is limited to regions (spots) of sizes well beyond that of a single cell, thus providing measurements for cell-aggregates which may mask critical interactions between neighboring cells of different types. While joint analysis with single cell RNA-sequencing (scRNA-seq) can be leveraged to alleviate this problem, current analyzes are limited to a discrete view of cell type proportion inside every spot. This limitation becomes critical in the common case where, even within a cell type, there is a continuum ofÂ  cell states, which can not be clearly demarcated and may reflect important differences in the cellsâ€™ function and interaction with their surrounding. To address this, we developed Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI), a probabilistic method for multi- resolution analysis for spatial transcriptomics, which explicitly models continuous variation within cell types. Using simulations, we demonstrate that DestVI is capable of providing higher resolution compared to the existing methods, and that it is also the first method to enable an estimate of gene expression by every cell type inside every spot. We then introduce an automated pipeline for analysis of a tissue, as well as comparison between tissues. We apply DestVI and this pipeline to study the response of lymph nodes to a pathogen and to explore the spatial organization of a mouse tumor model. In both cases, we demonstrate that DestVI can provide a reliable view of the organization of these tissues, and that it is capable of identifying important cell-type specific changes in gene expression - between different tissue regions or between conditions. DestVI is available as an open-source software in the scvi-tools codebase (https://scvi-tools.org).

overall_design:
  Lymph nodes from mice treated with mycobacterium or PBS or MCA205 tumor were used. Auricular LNs and the MCA205 tumor were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). Firstly, freshly obtained tissue samples were snap frozen in liquid nitrogen, then embedded in chilled Optimal Cutting Temperature compound (OCT; Tissue-Tek) and frozen on dry ice, then stored at -80脗掳C in a sealed container for later use. For Visium samples preparation, OCT-embedded tissue blocks were cut to 10 脗碌m thick using a LEICA CM1950 machine and mounted on the Visium spatial gene expression slide.

contributors:
  Romain Lopez;Hadas Keren-Shaul;Baoguo Li;Pierre Boyeau;Michael I Jordan;Merav Kedmi;David Pilzer;Allon Wagner;Yoseph Addad;Nir Yosef;Ido Amit

citation:
  Lopez, Romain et al. “DestVI identifies continuums of cell types in spatial transcriptomics data.” Nature biotechnology vol. 40,9 (2022): 1360-1369. doi:10.1038/s41587-022-01272-8


dataset_id: STDS0000085
species: Mus musculus
tissues: Brain
development_stages: P11;P14
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-06-28 00:00:00
last_modified: 2021-04-08 00:00:00
contacts: michael.ratz@ki.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153424
platforms: GPL16085;GPL16417;GPL21626;GPL24247
pmid: 35210624
has_paired: STDS0000085
title:
  Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

summary:
  We report TREX for simultaneous lineage tracking and expression profiling of dissociated cells from the juvenile mouse brain using single cell transcriptomics. We also developed Space-TREX enabling tracking and transcriptome profiling in intact tissue sections via Spatial Transcriptomics.

overall_design:
  Lentiviral delivery of a transcribed barcode into neuroepithelial progenitor cells using in utero microinjection into the mouse forebrain at embryonic day 9.5 followed by RNA-seq analysis of barcoded cells at postnatal day 11-14.

contributors:
  Michael Ratz;Leonie von Berlin;Ludvig Larsson;Marcel Martin;Jakub O Westholm;Gioele La Manno;Joakim Lundeberg;Jonas Frisén

citation:
  Ratz, Michael et al. “Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.” Nature neuroscience vol. 25,3 (2022): 285-294. doi:10.1038/s41593-022-01011-x


dataset_id: STDS0000078
title: Spatially mapped single-cell chromatin accessibility
species: Homo sapiens;Mus musculus
tissues: Cortex
organ_parts: Human cortex
technologies: sci-ATAC-seq;sciMAP-ATAC-seq
disease: Brain Cortex
overall_design: Single-cell ATAC-seq data including sci-ATAC-seq and sciMAP-ATAC-seq.
submission_date: 2021-01-14 00:00:00
last_modified: 2021-03-16 00:00:00
contributors: Andrew C Adey;Casey A Thornton
contacts: adey@ohsu.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164849
platforms: GPL18573;GPL19057
pmid: 33627658
summary:
  sciMAP-ATAC as a technology to produce single-cell ATAC-seq data with cells mapped to spatially-defined regions.

citation:
  Thornton, Casey A et al. “Spatially mapped single-cell chromatin accessibility.” Nature communications vol. 12,1 1274. 24 Feb. 2021, doi:10.1038/s41467-021-21515-7


dataset_id: STDS0000107
title: The spatial landscape of gene expression isoforms in tissue sections
species: Mus musculus
tissues: Brain
organ_parts: Olfactory bulb;Hippocampus
development_stages: 2 months
technologies: 10x Visium
disease: Olfactory bulb;Hippocampus
submission_date: 2020-07-06 00:00:00
last_modified: 2021-03-08 00:00:00
contributors: Kevin Lebrigand;Joseph Bergenstråhle;Kim Thrane;Pascal Babry;Rainer Waldmann;Joakim Lundeberg
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153859
platforms: GPL19057;GPL26624
pmid: 36928528
has_paired: SCDS0000042
summary:
  Mouse brain 10x Genomics Visium Spatial Transcriptomics profiles sequence either with Illumina for standard profiling and Nanopore promethION long read sequencer for full-length profiling.

overall_design:
  Visium Spatial Transcriptomics profiles of 2 mouse hippocampal samples (CBS1, CBS2) and 1 mouse olfactory bulk sample (MOB) sequence with short (illumina) and long (Nanopore) reads.

citation:
  Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A et al. The spatial landscape of gene expression isoforms in tissue sections. Nucleic Acids Res 2023 May 8;51(8):e47.


dataset_id: STDS0000089
title: Interleukin-17 governs hypoxic adaptation of injured epithelium [spatial transcriptomics]
species: Mus musculus
tissues: Skin
technologies: 10x Visium
disease: Skin injury
submission_date: 2021-02-17 00:00:00
last_modified: 2021-02-22 00:00:00
contributors: Piotr Konieczny;Xing Yue;Ikjot Sidhu;Shruti Naik
contacts: Shruti.Naik@nyulangone.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166948
platforms: GPL24247
pmid: 35709248
has_paired: SCDS0000043
summary:
  To define the gene signature and spatial architecture of the skin after injury, we performed spatial transcriptomics from mouse unwounded and wounded skin.

overall_design:
  Wild type (unwounded, wounded) and GFP-KI (wounded) skin were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing. The GFP-KI genotype disrupts the Rorc gene.

citation:
  Konieczny, Piotr et al. “Interleukin-17 governs hypoxic adaptation of injured epithelium.” Science (New York, N.Y.) vol. 377,6602 (2022): eabg9302. doi:10.1126/science.abg9302


dataset_id: STDS0000005
title: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
species: Homo sapiens
tissues: Brain
organ_parts: Dorsolateral prefrontal cortex
technologies: 10x Visium
disease: Schizophrenia and Autism spectrum disorder
submission_date: 2021-02-08 00:00:00
last_modified: 2021-02-08 00:00:00
accessions: http://research.libd.org/spatialLIBD/
pmid: 33558695
citation:
  Maynard, Kristen R et al. “Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex.” Nature neuroscience vol. 24,3 (2021): 425-436. doi:10.1038/s41593-020-00787-0


dataset_id: STDS0000004
species: Mus musculus
tissues: Brain
cell_types: astrocytes;oligodendrocytes;populations of vascular and immune cells;neuronal types
technologies: 10x Visium;scRNA
disease: Brain Cortex
submission_date: 2020-09-23 00:00:00
last_modified: 2021-02-01 00:00:00
contributors: Joglekar A;Collier P;Tilgner H
contacts: anj2026@med.cornell.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158450
platforms: Illumina HiSeq 4000;Illumina NovaSeq 6000;PromethION
pmid: 33469025
has_paired: SCDS0000046
title:
  A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

summary:
  Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7. Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain (www.isoformAtlas.com). Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function.

overall_design:
  10x single-cell sequencing done on two replicates of Hippocampus and Prefrontal Cortex (PFC) samples. PacBio sequencing done on the same cDNA to get long read expression data in single cells. Spatial sequencing was conducted using 10x visium sequencing on brain slices, followed by PacBio and Oxford Nanopore sequencing on the same cDNA

citation:
  Joglekar, Anoushka et al. “A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.” Nature communications vol. 12,1 463. 19 Jan. 2021, doi:10.1038/s41467-020-20343-5


dataset_id: STDS0000008
species: Mus musculus
tissues: Kidney
cell_types: renal epithelial;immune;endothelial
sex: Male
technologies: Spatial Transcriptomics;scRNA
disease: Acute kidney injury
submission_date: 2020-07-09 00:00:00
last_modified: 2021-01-16 00:00:00
contributors: Janosevic D;Hato T;McCarthy T
platforms: Illumina NovaSeq 6000
pmid: 33448928
title:
  The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline

summary:
  Clinical sepsis is a highly dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single cell RNA sequencing and spatial transcriptomics revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. We identified key changes in gene expression that altered cellular functions and can explain features of clinical sepsis. These changes converged towards a remarkable global cell-cell communication failure and organ shutdown at a well-defined point in the sepsis timeline. Importantly, this time point was also a transition towards the emergence of recovery pathways. This rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis.

overall_design:
  The 129sv mouse was sacrificed 6 hours after cecal ligation puncture and tissue was placed in an OCT mold and stored at -80 C. A septic mouse kidney was immediately frozen in Optimal Cutting Temperature media (O.C.T.). A 10 渭m frozen tissue section was cut and affixed to a Visium Spatial Gene Expression library preparation slide (Catalogue # 1000200, 10x Genomics, Pleasanton, California, USA). The specimen was fixed in methanol and stained with hematoxylin-eosin reagents. Images of hematoxylin-eosin-labeled tissues were collected as mosaics of 10x fields using a Keyence BZ-X810 fluorescence microscope equipped with a Nikon 10x CFI Plan Fluor objective. The tissue was then permeabilized for 12 minutes and RNA was isolated. The cDNA libraries were prepared and then sequenced on an Illumina NovaSeq 6000. Using Seurat 3.1.4, we identified anchors between the integrated single cell object and the spatial transcriptomics datasets and used those to transfer the cluster data from the single cell to the spatial transcriptomics. For each spatial transcriptomics spot, this transfer assigns a score to each single cell cluster. We selected the cluster with the highest score in each spot to represent its single cell associated cluster. Using a Loupe Browser, expression data was visualized overlying the hematoxylin-eosin image.

citation:
  Janosevic, Danielle et al. “The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline.” eLife vol. 10 e62270. 15 Jan. 2021, doi:10.7554/eLife.62270

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154107;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151658


dataset_id: STDS0000168
title: Soybean Organ Transcriptomic Atlas
species: Glycine max
tissues: Plant part
organ_parts: Root;SAM;Nodule;Leaf;Stem
development_stages: VC
technologies: Stereo-Seq;scRNA
disease: Plants
submission_date: 2022-12-19 00:00:00
last_modified: 2020-12-19 00:00:00
contributors: Jingwei Fan , Yanting Shen , Chuan Chen , Xi Chen , Xun Xu , Xin Liu , Zhixi Tian
contacts: xuxun@genomics.cn , liuxin@genomics.cn , zxtian@genetics.ac.cn
platforms: DNBSEQ-T1, DNBSEQ-T7 , DNBSEQ-T10 , DNBSEQ-G400(MGISEQ-2000)
summary:
  Disclosing Revealing the temporal and spatial expression of each gene is predominantly importantcritical for the understanding of plant organ development. To this end, There is increasing demand for the construction of an integrated transcriptomic atlases using different multiple types of transcriptome data as a means of achieving this aim is increasingly demanded.   in increasing demand. In this study, we sequencesequenced 315 soybean tissues during over the course of the full whole developmental cycle by bulk RNA-seq and sequencesequenced 5 representative organs (root, noduleroots, nodules, shoot apical meristem, leaf and stemmeristems, leaves and stems) by snRNA-seq and Stereo-seq, respectively. Integrating these transcriptome data, we constructconstructed a comprehensive soybean transcriptomic atlases. TakenTaking the investigations of genes related to blade, vascular bundles and nodule development as examples, we demonstrate that thean integrating of integrated transcriptomic atlas has robust powerful potential for in exploring key genes in organ formation. Together, the panoramic soybean transcriptomic atlases provides a valuable resource and wouldwill greatly promote the functional studystudies in the future.

overall_design:
  Roots, stems, leaves, shoot apical meristems and nodule from the vegetative cotyledon stages of Glycine max Zhonghuang 13 were fresh frozen and sectioned at 10μm thickness onto spatial transcriptomics (ST) slides for mRNA capture, and the nucleus was dissociated to prepare a single cell suspension for mRNA capture, followed by library preparation and sequencing.


dataset_id: STDS0000075
title: High spatial resolution multi-omics atlas sequencing of mouse embryos
species: Mus musculus
tissues: Embryo
development_stages: E10;E12;E11
technologies: DBiT-seq
disease: Embryo development
submission_date: 2019-09-25 00:00:00
last_modified: 2020-12-16 00:00:00
contributors: Rong Fan;Yang Liu;Mingyu Yang;Yanxiang Deng
contacts: mingyu.yang@yale.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137986
platforms: Illumina HiSeq 4000
pmid: 33188776
has_paired: STDS0000075
summary:
  Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.

overall_design:
  Applying new approach 鈥?microfluidic Deterministic Barcoding in Tissue for spatial omics sequencing to mouse embryo tissues in different resolution (10渭m, 25渭m, 50渭m).

citation:
  Liu, Yang et al. “High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.” Cell vol. 183,6 (2020): 1665-1681.e18. doi:10.1016/j.cell.2020.10.026


dataset_id: STDS0000072
title: LCM-Seq analysis of microscopically defined human embryo HSC microenvironment
species: Homo sapiens
tissues: Dorsal aorta
cell_types: CS17;CS16
technologies: LCM-seq
disease: Embryo development
submission_date: 2020-06-05 00:00:00
last_modified: 2020-12-01 00:00:00
contributors: Edie I Crosse;Alexander Medvinsky
contacts: edie.crosse@outlook.com
platforms: Illumina HiSeq 4000;Illumina NovaSeq 6000
pmid: 32946788
summary:
  This dataset contains RNA-Seq data for cells within spatially defined subdomains of the human embryo dorsal aorta, subdissected from tissue sections using laser capture microdissection. This dataset explores dorsal-ventral polarisation across the dorsal aorta, the site of hematopoietic stem cell emergence.

overall_design:
  In total 30 samples (subdomains) from 6 human embryos are analysed. This includes 6 subdomains (V_Inner, D_Inner, V_Mid, D_Mid, V_Outer, D_Outer) from 3 CS16 embryos and 4 subdomains ([V], [VL], [DL], [D]) from 3 CS17 embryos.

citation:
  Crosse, Edie I et al. “Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development.” Cell stem cell vol. 27,5 (2020): 822-839.e8. doi:10.1016/j.stem.2020.08.004

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151875;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151877


dataset_id: STDS0000001
title: Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
species: Homo sapiens
tissues: Skin
sex: Unknown
technologies: 10x Visium;Spatial Transcriptomics;scRNA
disease: Squamous cell carcinoma
submission_date: 2020-01-24 00:00:00
last_modified: 2020-11-18 00:00:00
contributors: Andrew Ji
contacts: andrewji@stanford.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144239
platforms: Illumina NextSeq 500
pmid: 32579974
has_paired: SCDS0000044
cell_types:
  fibroblasts;endothelial cells;melanocytes;CLEC9A;CD1C;plasmacytoid;AXL+SIGLEC6+ (AS) dendritic cells (DCs)

summary:
  To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and site-matched normal skin

overall_design:
  Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing

citation:
  Ji, Andrew L et al. “Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.” Cell vol. 182,2 (2020): 497-514.e22. doi:10.1016/j.cell.2020.05.039


dataset_id: STDS0000073
species: Homo sapiens
tissues: Pancreas
organ_parts: Pancreatic adenocarcinoma
technologies: Spatial Transcriptomics
disease: Pancreatic cancer
submission_date: 2018-03-02 00:00:00
last_modified: 2020-11-05 00:00:00
contributors: Reuben Moncada
contacts: itai.yanai@nyumc.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111672
platforms: Illumina NextSeq 500
pmid: 31932730
has_paired: STDS0000073
title:
  Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

summary:
  Single-cell RNA sequencing (scRNA-seq) enables the systematic identification of cell populations in a tissue, but characterizing their spatial organization remains challenging. We combine a microarray-based spatial transcriptomics method that reveals spatial patterns of gene expression using an array of spots, each capturing the transcriptomes of multiple adjacent cells, with scRNA-Seq generated from the same sample. To annotate the precise cellular composition of distinct tissue regions, we introduce a method for multimodal intersection analysis. Applying multimodal intersection analysis to primary pancreatic tumors, we find that subpopulations of ductal cells, macrophages, dendritic cells and cancer cells have spatially restricted enrichments, as well as distinct coenrichments with other cell types. Furthermore, we identify colocalization of inflammatory fibroblasts and cancer cells expressing a stress-response gene module. Our approach for mapping the architecture of scRNA-seq-defined subpopulations can be applied to reveal the interactions inherent to complex tissues.

overall_design:
  Single-cell RNA-sequencing and spatial transcriptomics of primary pancreatic cancer tissue from six patients. 2018-03-12

citation:
  Moncada, Reuben et al. “Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.” Nature biotechnology vol. 38,3 (2020): 333-342. doi:10.1038/s41587-019-0392-8


dataset_id: STDS0000132
title: Spatial transcriptome of FFPE sample by DBiT-seq
species: Mus musculus
tissues: Embryo
organ_parts: Mouse Embryo;Mouse atrium;Mouse ventricle;Mouse aorta
technologies: DBiT-seq
disease: Embryo development
submission_date: 2020-08-25 00:00:00
last_modified: 2020-11-01 00:00:00
contributors: Fan Rong;Liu Yang
contacts: yang.liu.yl2224@yale.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156862
platforms: GPL21103
summary:
  Here, we show that DBiT-seq (Deterministic barcoding in tissue) can be applied to FFPE samples, providing quality transcriptome information. We first studied the E10.5 mouse embryo tissue section with a 25 µm pixel size chip and identified all the major anatomical structures. Then, we analyzed the three major components of mouse heart and circulatory system: aorta, atrium, and ventricle.  Results show that major cell types in all above tissue types can be identified after integration with published scRNA-seq reference data.

overall_design:
  Spatial transcriptome of FFPE sample, including mosue embryo E10.5, adult mouse aorta, artrium and ventricle


dataset_id: STDS0000045
title: Human Cerebellum: Targeted, Neuroscience Panel
species: Homo sapiens
tissues: Brain
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Homo sapiens cerebellum tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_Cerebellum_Neuroscience


dataset_id: STDS0000044
title: Human Cerebellum: Whole Transcriptome Analysis
species: Homo sapiens
tissues: Brain
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Homo sapiens cerebellum tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_Cerebellum


dataset_id: STDS0000043
species: Homo sapiens
tissues: Spinal cord
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
title:
  Human Spinal Cord: Targeted, Neuroscience Panel. Stains: DAPI, Anti-SNAP25, Anti-GFAP, Anti-Myelin CNPase

summary:
  10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_SpinalCord_Neuroscience


dataset_id: STDS0000042
species: Homo sapiens
tissues: Spinal cord
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
title:
  Human Spinal Cord: Whole Transcriptome Analysis. Stains: DAPI, Anti-SNAP25, Anti-GFAP, Anti-Myelin CNPase

summary:
  10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).10x Genomics obtained fresh frozen Homo sapiens spinal cord tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_SpinalCord


dataset_id: STDS0000041
title: Human Glioblastoma: Targeted, Pan-Cancer Panel
species: Homo sapiens
tissues: Brain
organ_parts: Glioblastoma multiforme tissue
technologies: 10x Visium
disease: Glioblastoma
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen human glioblastoma multiforme tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_Glioblastoma_Pan_Cancer


dataset_id: STDS0000040
title: Human Glioblastoma: Whole Transcriptome Analysis
species: Homo sapiens
tissues: Brain
organ_parts: Glioblastoma multiforme tissue
technologies: 10x Visium
disease: Glioblastoma
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen human glioblastoma multiforme tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_Glioblastoma


dataset_id: STDS0000039
title: Human Breast Cancer: Targeted, Immunology Panel
species: Homo sapiens
tissues: Breast
technologies: 10x Visium
disease: Breast cancer
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
has_paired: SCDS0000018
summary:
  10x Genomics obtained fresh frozen human Invasive Lobular Carcinoma breast tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_BreastCancer_Immunology


dataset_id: STDS0000038
title: Human Breast Cancer: Whole Transcriptome Analysis
species: Homo sapiens
tissues: Breast
technologies: 10x Visium
disease: Breast cancer
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
has_paired: SCDS0000018
summary:
  10x Genomics obtained fresh frozen human Invasive Lobular Carcinoma breast tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_BreastCancer


dataset_id: STDS0000037
title: Human Ovarian Cancer: Targeted, Pan-Cancer Panel. Stains: DAPI, Anti-PanCK, Anti-CD45
species: Homo sapiens
tissues: Ovarian
technologies: 10x Visium
disease: Endometrial Adeno carcinoma
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Endometrial Adenocarcinoma of the ovary tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312). The tissue was AJCC/UICC T1N0M0, Stage Group I.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_OvarianCancer_Pan_Cancer


dataset_id: STDS0000036
title: Human Ovarian Cancer: Targeted, Immunology Panel. Stains: DAPI, Anti-PanCK, Anti-CD45
species: Homo sapiens
tissues: Ovarian
technologies: 10x Visium
disease: Endometrial Adeno carcinoma
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Endometrial Adenocarcinoma of the ovary tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312). The tissue was AJCC/UICC T1N0M0, Stage Group I.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_OvarianCancer_Immunology


dataset_id: STDS0000035
title: Human Ovarian Cancer: Whole Transcriptome Analysis. Stains: DAPI, Anti-PanCK, Anti-CD45
species: Homo sapiens
tissues: Ovarian
technologies: 10x Visium
disease: Endometrial Adeno carcinoma
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Endometrial Adenocarcinoma of the ovary tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312). The tissue was AJCC/UICC T1N0M0, Stage Group I.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_OvarianCancer


dataset_id: STDS0000034
title: Human Colorectal Cancer: Targeted, Gene Signature Panel
species: Homo sapiens
tissues: Intestine
technologies: 10x Visium
disease: Colorectal cancer
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Invasive Adenocarcinoma of the large intestine tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_ColorectalCancer_GeneSignature


dataset_id: STDS0000033
title: Human Colorectal Cancer: Whole Transcriptome Analysis
species: Homo sapiens
tissues: Intestine
technologies: 10x Visium
disease: Colorectal cancer
submission_date: 2020-10-27 00:00:00
last_modified: 2020-10-27 00:00:00
summary:
  10x Genomics obtained fresh frozen Invasive Adenocarcinoma of the large intestine tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Parent_Visium_Human_ColorectalCancer


dataset_id: STDS0000068
species: Homo sapiens
tissues: Liver
organ_parts: Liver;Fetal liver
technologies: GeoMx DSP
disease: Hepatocellular Carcinoma
submission_date: 2020-08-21 00:00:00
last_modified: 2020-09-27 00:00:00
contacts: sharmaa@gis.a-star.edu.sg
platforms: Multiplex spatial transcriptomics assay
pmid: 32976798
title:
  Onco-fetal reprogramming of endothelial cells drives immunosuppressive macrophages in Hepatocellular Carcinoma (Nanostring)

summary:
  Liver dysfunction is associated with diseases ranging from metabolic disorders to hepatocellular carcinomas (HCC). Here we employed single-cell RNA-sequencing to extensively characterise the cellular landscape of human liver, from development to disease. We analysed ~212,000 cells representing human fetal liver, HCC and mouse liver. Our analysis revealed a remarkable fetal-like reprogramming of the tumor microenvironment (TME). Specifically, the HCC ecosystem displayed features reminiscent of fetal development, including the re-emergence of fetal-associated endothelial cells (PLVAP+/VEGFR2+), and fetal-like (FOLR2+) tumor-associated macrophages (TAMs). In a cross-species comparative analysis, we discovered remarkable similarity of gene expression and regulatory networks between mouse embryonically-seeded, fetal-liver and FOLR2+ tumor macrophages. Spatial transcriptomics further corroborated a shared onco-fetal ecosystem between fetal-liver and HCC. Furthermore, gene regulatory analysis, spatial transcriptomics, and in vitro functional assays implicated VEGF and NOTCH signaling in maintaining onco-fetal ecosystem. Taken together, we report a shared immunosuppressive onco-fetal ecosystem between the human fetal-liver and HCC. Our results unravel a previously unexplored onco-fetal reprogramming of tumor ecosystem, provides a novel target for therapeutic interventions in HCC and also opens up avenues for identifying similar paradigms in other cancers and disease states.

overall_design:
  Analysis of hepatocellular carcinoma (HCC) and human fetal liver samples ,Tissue slides from 3 HCC patients (adjacent normal & tumor section for each) and 3 human fetal liver samples were used for this experiment. 12 regions of interests were selected for each of the 9 samples so a total of 108 regions of interests were analysed. The samples were stained with 96 targets (immune, stromal, epithelial and onco-fetal markers).

contributors:
  Sharma A;Seow JW;Dutertre C;Pai R;Blériot C;Mishra A;Wong RM;Singh GS;Sudhagar S;Khalilnezhad S;Erdal S;Teo HM;Khalilnezhad A;Chakarov S;Lim TK;Chung AY;Kow AW;Cheow PC;Bonney GK;Goh BK;Chan JK;Chow PK;Ginhoux F;DasGupta R

citation:
  Sharma, Ankur et al. “Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma.” Cell vol. 183,2 (2020): 377-394.e21. doi:10.1016/j.cell.2020.08.040

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156626;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156625


dataset_id: STDS0000012
species: Mus musculus
tissues: Brain
organ_parts: Hippocampus;Olfactory bulb
sex: Male
technologies: Spatial Transcriptomics
disease: Alzheimer disease
submission_date: 2020-09-21 00:00:00
last_modified: 2020-09-21 00:00:00
contributors: Jose Fernandez Navarro
accessions: https://data.mendeley.com/datasets/6s959w2zyr/1
pmid: 33083725
title:
  Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease

summary:
  This is the public data repository for the the work presented in Navarro and Croteau et al. iScience, 2020. https://doi.org/10.1016/j.isci.2020.101556

  The repository contains 48 Spatial Tancriptomics (ST) sections (24 of the hippocampus and 24 of the olfactory bulb). 

  The sections were obtained from an Alzheimer´s disease mouse model:

  3xAD, 3xPB, 3xPB and WT

  For each section, we have deposited the following:

  - H&E file
  - Matrix of counts

  We also included the merged matrices of counts and meta files. 

  The results of the analyses are also present (factor analysis clusters, DE analysis genes, pathways, etc...).

  License:CC BY 4.0(https://creativecommons.org/licenses/by/4.0/) 

citation:
  Navarro, José Fernández et al. “Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease.” iScience vol. 23,10 101556. 15 Sep. 2020, doi:10.1016/j.isci.2020.101556


dataset_id: STDS0000070
species: Danio rerio;Gallus gallus;Homo sapiens;Mus musculus
tissues: Embryo
development_stages: 3 days;4 days
technologies: Tomo-seq
disease: Normal atlas
submission_date: 2019-03-15 00:00:00
last_modified: 2020-09-07 00:00:00
contacts: c.robin@hubrecht.eu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128350
platforms: Illumina HiSeq 2500;Illumina NextSeq 500
pmid: 32457985
title:
  Multi-species tomo-sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta

summary:
  Spatial transcriptomics by RNA-tomography (Tomo-seq) on whole or sub-dissected embryos (processed along the anterior-to-posterior axis) and on transversal thick slices (processed along the dorsal-to-ventral axis).  2019-03-15

contributors:
  Laurent Yvernogeau;Ismaël Morin-Poulard;Anna Klaus;Joris Maas;Stefan Schulte-Merker;Eugene Berezikov;Jan P Junker;Catherine Robin

citation:
  Yvernogeau, Laurent et al. “Multispecies RNA tomography reveals regulators of hematopoietic stem cell birth in the embryonic aorta.” Blood vol. 136,7 (2020): 831-844. doi:10.1182/blood.2019004446


dataset_id: STDS0000055
species: Mus musculus
tissues: Embryo
organ_parts: Gastrulation
development_stages: E7.0
technologies: Geo-seq
disease: Embryonic brain
submission_date: 2015-02-13 00:00:00
last_modified: 2020-08-11 00:00:00
contributors: Peng G;Suo S;Chen J;Jing N;Han JJ
contacts: guangdun.peng@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65924
pmid: 27003939
title:
  Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

summary:
  To glean an appreciation of the holistic genetic activity in the gastrulating Mus musculus embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D transcriptome reveals that (i) the epiblast is partitioned into transcription domains corresponding to regions of epiblast where cells are endowed specifically with ectoderm and mesendoderm potency, (ii) novel lineage markers are identified as genes expressed in epiblast domains populated by cells displaying different lineage fates, (iii) functionally related gene regulatory circuitry and signaling pathways are acting in concert in the transcriptional domains, and (iv) the spatial information provides reference zipcodes for mapping the prospective address of cell samples from different embryos and stem cell lines. The quantified expression data can also be visualized as “3D digitized whole mount in situ hybridization” of all the expressed transcripts in the epiblast.

overall_design:
   (i) By using lasermicrodissection, we carried out transcriptome profiling on embryo sections at a high resolution of ~20 cells per sample with the spatial information preserved. We then constructed a comprehensive spatial transcriptome map in the midgastrulation embryo that is visualized in a 3D embryonic model based on the sequencing data.
  Embryo position (A/L/P/R) and section (111) descriptors:
  A stands for laser capture microdissected samples from the anterior epiblast of the embryo; P for posterior; L for the left lateral epiblast of the embryo; R for the right lateral. The section is collected from distal to proximal, and the section 1 to 11 is the cryosection order, covering the whole embryonic part of a late midstreak embryo. Section 1 is the most distal section and 11 is the most proximal section. Please be aware that the labels for left (L) and right (R) are from mirrored images and should be considered as right and left positions in real embryo settings. Anterior (A) or Posterior (P) regions do not change.
  (ii) Additional samples are RNAseq data of 70 single cells from E7.0 Mus musculus embryo. These 70 samples were randomly picked from the anterior or posterior embryonic half.

citation:
  Peng, Guangdun et al. “Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo.” Developmental cell vol. 36,6 (2016): 681-97. doi:10.1016/j.devcel.2016.02.020


dataset_id: STDS0000077
title: Molecular architecture of lineage specification and tissue organization in early mouse embryo
species: Mus musculus
tissues: Embryo
organ_parts: Embryo
cell_types: Mouse embryonic cells
development_stages: E5.5;E6.0;E6.5;E7.0;E7.5
technologies: Geo-seq
disease: Embryonic brain
submission_date: 2018-10-09 00:00:00
last_modified: 2020-08-05 00:00:00
contributors: Guangdun Peng;Guizhong Cui;Shengbao Suo;Naihe Jing;Jing-Dong J Han
contacts: guangdun.peng@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120963
platforms: Illumina HiSeq 2500;Illumina NovaSeq 6000
pmid: 31391582
summary:
  During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.

overall_design:
  By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data. Please be aware that the positions for left (L) and right (R) are from mirrored images and should be considered as right and left in real embryo settings. Anterior (A) or Posterior (P) regions do not change. 

citation:
  Peng, Guangdun et al. “Molecular architecture of lineage allocation and tissue organization in early mouse embryo.” Nature vol. 572,7770 (2019): 528-532. doi:10.1038/s41586-019-1469-8


dataset_id: STDS0000084
title: Spatial Transcriptomics and In Situ Sequencing to Study Alzheimerâ€™s Disease
species: Mus musculus
tissues: Brain
development_stages: 3 months;6 months;12 months;18 months
technologies: Spatial Transcriptomics
disease: Alzheimer disease
submission_date: 2020-06-15 00:00:00
last_modified: 2020-07-22 00:00:00
contacts: bart.destrooper@kuleuven.vib.be
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152506
platforms: GPL19057
pmid: 32702314
summary:
  While complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here in an AD mouse model the transcriptional changes occurring in tissue domains of 100 Î¼m diameter around the amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIG), while a multicellular gene co- expression network of Plaque-Induced Genes (PIGs) involving the complement system, oxidative stress, lysosomes and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomic analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.

overall_design:
  In situ 2D-RNAseq via Spatial Transcriptomics  on coronal section of AppNL-G-F KI mice and C57Bl/6J  mice at 3,6,12 and 18 months of age.

contributors:
  Wei-Ting Chen;Ashley Lu;Katleen Craessaerts;Benjamin Pavie;Carlo S Frigerio;Nikky Corthout;Xiaoyan Qian;Jana Lalakova;Malte Kühnemund;Iryna Voytyuk;Leen Wolfs;An Snellinx;Sebastian Munck;Aleksandra Jurek;Jose F Navarro;Takaomi C Saido;Joakim Lundeberg;Mark Fiers;Bart De Strooper

citation:
  Chen, Wei-Ting et al. “Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease.” Cell vol. 182,4 (2020): 976-991.e19. doi:10.1016/j.cell.2020.06.038


dataset_id: STDS0000169
title: Molecular Atlas of the Adult Mouse Brain
species: Mus musculus
development_stages: 9 weeks
sex: Male
technologies: Spatial Transcriptomics
disease: Normal atlas
submission_date: 2020-03-30 00:00:00
last_modified: 2020-07-13 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147747
platforms: Illumina NextSeq 500
pmid: 32637622
summary:
  Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette – that is sufficient to spatially annotate the adult brain. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.

overall_design:
  We hybridized 75 coronal sections from one brain hemisphere of 3 adult mice with Spatial Transcriptomics and defined a molecular atlas using clustering algorithms.

contributors:
  Meletis, Konstantinos;Ortiz, Cantin;Fernandez Navarro, Jose;Jurek, Aleksandra;Märtin, Antje;Lundeberg, Joakim

citation:
  Ortiz, Cantin et al. “Molecular atlas of the adult mouse brain.” Science advances vol. 6,26 eabb3446. 26 Jun. 2020, doi:10.1126/sciadv.abb3446


dataset_id: STDS0000066
title: Molecular atlas of the adult mouse brain.
species: Mus musculus
tissues: Brain
development_stages: 9 weeks
sex: Male
technologies: Spatial Transcriptomics
disease: Normal atlas
submission_date: 2020-03-30 00:00:00
last_modified: 2020-07-13 00:00:00
contacts: dinos.meletis@ki.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147747
platforms: Illumina NextSeq 500
pmid: 32637622
has_paired: SCDS0000016
summary:
  Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette – that is sufficient to spatially annotate the adult brain. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.

overall_design:
  We hybridized 75 coronal sections from one brain hemisphere of 3 adult mice with Spatial Transcriptomics and defined a molecular atlas using clustering algorithms.

contributors:
  Cantin Ortiz;Jose Fernandez Navarro;Aleksandra Jurek;Antje Märtin;Joakim Lundeberg;Konstantinos Meletis

citation:
  Ortiz, Cantin et al. “Molecular atlas of the adult mouse brain.” Science advances vol. 6,26 eabb3446. 26 Jun. 2020, doi:10.1126/sciadv.abb3446


dataset_id: STDS0000032
title: Adult Human Brain 1 (Cerebral Cortex, Unknown orientation). Stains: Anti-GFAP, Anti-NFH
species: Homo sapiens
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Brain_Section_1
summary:
  10 µm cerebral cortex section of human brain was obtained from tissue blocks purchased from BioIVT. The section was stained with antibodies and DAPI following Visium Spatial Protocols Tissue Preparation Guide (CG000240) with Methanol Fixation, Immunofluorescence Staining and Imaging for Visium Spatial Protocols (CG000312).


dataset_id: STDS0000030
title: Adult Mouse Brain Section 2 (Coronal). Stains: DAPI, Anti-GFAP, Anti-NeuN
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  Adult 10 µm coronal section of mouse brain was obtained from tissue blocks purchased from BioIVT. The section was stained with antibodies and DAPI following Visium Spatial Protocols Tissue Preparation Guide (CG000240) with Methanol Fixation, Immunofluorescence Staining and Imaging for Visium Spatial Protocols (CG000312).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain_Coronal_Section_2


dataset_id: STDS0000029
title: Adult Mouse Brain Section 1 (Coronal). Stains: DAPI, Anti-NeuN
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  Adult 10 µm coronal section of mouse brain was obtained from tissue blocks purchased from BioIVT. The section was stained with antibodies and DAPI following Visium Spatial Protocols Tissue Preperation Guide (CG000240) with Methanol Fixation, Immunofluorescence Staining and Imaging for Visium Spatial Protocols (CG000312).

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain_Coronal_Section_1


dataset_id: STDS0000027
title: Human Breast Cancer (Block A Section 1)
species: Homo sapiens
tissues: Breast
technologies: 10x Visium
disease: Invasive Ductal carcinoma
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000018
summary:
  10x Genomics obtained fresh frozen Invasive Ductal Carcinoma breast tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Breast_Cancer_Block_A_Section_1


dataset_id: STDS0000026
title: Human Breast Cancer (Block A Section 2)
species: Homo sapiens
tissues: Breast
technologies: 10x Visium
disease: Invasive Ductal carcinoma
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000018
summary:
  10x Genomics obtained fresh frozen Invasive Ductal Carcinoma breast tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Breast_Cancer_Block_A_Section_2


dataset_id: STDS0000025
title: Human Heart
species: Homo sapiens
tissues: Heart
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Heart
has_paired: SCDS0000047
summary:
  10x Genomics obtained fresh frozen human heart tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.


dataset_id: STDS0000024
title: Human Lymph Node
species: Homo sapiens
tissues: Lymph
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Human_Lymph_Node
has_paired: STDS0000152
summary:
  10x Genomics obtained fresh frozen human lymph node tissue from BioIVT Asterand Human Tissue Specimens. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.


dataset_id: STDS0000023
title: Mouse Kidney Section (Coronal)
species: Mus musculus
tissues: Kidney
technologies: 10x Visium
disease: Normal atlas
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Mouse_Kidney
has_paired: SCDS0000039
summary:
  10x Genomics obtained fresh frozen mouse kidney tissue (Strain C57BL/6)from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.


dataset_id: STDS0000022
title: Mouse Brain Section (Coronal)
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
accessions: https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain
has_paired: SCDS0000016
summary:
  10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6)from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness from a slice of the coronal plane were placed on Visium Gene Expression Slides.


dataset_id: STDS0000021
title: Mouse Brain Serial Section 1 (Sagittal-Posterior)
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6) from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness from a sagittal slice of the posterior were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Mouse_Brain_Sagittal_Posterior


dataset_id: STDS0000020
title: Mouse Brain Serial Section 2 (Sagittal-Posterior)
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6) from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness from a sagittal slice of the posterior were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Mouse_Brain_Sagittal_Posterior_Section_2


dataset_id: STDS0000019
title: Mouse Brain Serial Section 2 (Sagittal-Anterior)
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6)from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness from a sagittal slice of the anterior were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Mouse_Brain_Sagittal_Anterior_Section_2


dataset_id: STDS0000018
title: Mouse Brain Serial Section 1 (Sagittal-Anterior)
species: Mus musculus
tissues: Brain
technologies: 10x Visium
disease: Brain Cortex
submission_date: 2020-06-23 00:00:00
last_modified: 2020-06-23 00:00:00
has_paired: SCDS0000016
summary:
  10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6)from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10 µm thickness from a sagittal slice of the anterior were placed on Visium Gene Expression Slides.

accessions:
  https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Mouse_Brain_Sagittal_Anterior


dataset_id: STDS0000134
species: Homo sapiens
tissues: Stress granules
cell_types: cell line:HEK293T
technologies: APEX-seq
disease: Normal atlas
submission_date: 2018-10-22 00:00:00
last_modified: 2020-06-07 00:00:00
contributors: Alejandro Padron;Shintaro Iwasaki;Nicholas Ingolia
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121575
platforms: GPL21103
pmid: 31442426
title:
  Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

summary:
  Stress granules are dynamic non-membrane bound organelles made up of untranslating messenger ribonucleoproteins (mRNPs) that form when cells integrate stressful environmental cues resulting in stalled translation initiation complexes. Although stress granules dramatically alter mRNA and protein localization, understanding these complexes has proven to be challenging through conventional imaging, purification, and crosslinking approaches. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching both the spatial transcriptome using APEX-seq, and the spatial proteome using APEX-mass spectrometry (APEX-MS) provide new insights into the organization of translation initiation complexes on active mRNAs, as well as revealing unanticipated complexity in stress granule contents, and provides a powerful approach to explore the spatial environment of macromolecules.

overall_design:
  APEX-eIF4E, APEX-eIF4A, APEX-GFP, C1-APEX, and APEX-CBX1 under Naive conditions were used to assess within and between compartment differnces were performed in duplicate with their corresponding input samples using a Hiseq4000. RNA from APEX-eIF4A under heatshock or hippuristanol samples were performed in duplicate using a Hiseq4000

citation:
  Padrón, Alejandro et al. “Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules.” Molecular cell vol. 75,4 (2019): 875-887.e5. doi:10.1016/j.molcel.2019.07.030


dataset_id: STDS0000003
species: Gallus gallus
tissues: Embryo
organ_parts: Heart
cell_types: C2;C3
development_stages: HH21-HH24;HH30-HH31;HH35-HH36;HH40
technologies: 10x Visium;scRNA
disease: Heart development
submission_date: 2020-04-27 00:00:00
last_modified: 2020-05-06 00:00:00
contributors: Mantri M;Scuderi GJ;Nassab RA;Butcher JT;De Vlaminck I
contacts: id93@cornell.edu
platforms: Illumina NextSeq 500
pmid: 33741943
has_paired: STDS0000003
title:
  Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

summary:
  Spatially-resolved RNA-seq with high-throughput time-course scRNA-seq to study the gene expression, interactions, and regulatory programs that drive fetal development of the chicken hearts.

overall_design:
  Spatially-resolved RNA-seq with high-throughput time-course scRNA-seq to study the gene expression, interactions, and regulatory programs that drive fetal development of the chicken hearts.

citation:
  Mantri, Madhav et al. “Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis.” Nature communications vol. 12,1 1771. 19 Mar. 2021, doi:10.1038/s41467-021-21892-z

accessions:
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149457;https://github.com/madhavmantri/chicken_heart 


dataset_id: STDS0000074
title: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids
species: Homo sapiens;Mus musculus
tissues: Gastrula
organ_parts: Gastruloid
technologies: Tomo-seq
disease: Normal atlas
submission_date: 2018-11-30 00:00:00
last_modified: 2020-04-15 00:00:00
contacts: a.alemany@hubrecht.eu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123187
platforms: Illumina NextSeq 500
pmid: 32076263
summary:
  Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization.  Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos.  

overall_design:
  RNA sequencing data from tissue sections isolated from mouse gastruloids (tomo-seq and scRNA-seq) | For mGst-Lfng-* samples, each processed data was generated from both run1 and run2 samples, and is linked to the corresponding run1 sample records.

contributors:
  Susanne C van den Brink;Anna Alemany;Vincent van Batenburg;Naomi Moris;Marloes Blotenburg;Judith Vivié;Peter Baillie-Johnson;Jennifer Nichols;Katharina F Sonnen;Alfonso Martinez-Arias;Alexander van Oudenaarden

citation:
  van den Brink, Susanne C et al. “Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids.” Nature vol. 582,7812 (2020): 405-409. doi:10.1038/s41586-020-2024-3


dataset_id: STDS0000113
title: Human Cervical Cancer (FFPE)
species: Homo sapiens
tissues: Cervical
organ_parts: Cervical cancer
cell_types: squamous cell
technologies: 10x Visium
disease: Cervical cancer
submission_date: 2020-03-29 00:00:00
last_modified: 2020-03-29 00:00:00
contributors: Eadon Michael;Ricardo Melo Ferreira;Ying-Hua Cheng
accessions: https://www.10xgenomics.com/resources/datasets/human-cervical-cancer-1-standard
platforms: Illumina NovaSeq 6000
has_paired: SCDS0000045
summary:
  5 µm section from squamous cell carcinoma of human cervical cancer. FFPE tissue purchased from Discovery Life Sciences.

  Block C00084155.1a
  Cervical Cancer, Invasive. Squamous cell carcinoma T1bN0M0 IB
  Brightfield camera, Magnification: 20x
  Sequencing instrument: Illumina NovaSeq 6000, flow cell HVFG7DSXY (lanes 1-4)
  Sequencing depth: 72,087 reads per spot
  Sequencing configuration: 28 bp read 1 (16 bp Visium spatial barcode, 12 bp UMI), 50 bp read 2 (transcript), 10 bp i7 sample barcode and 10 bp i5 sample barcode
  Dual-Index set: SI-TS-E5
  Slide: V10L13-019
  Area: A1            This dataset is licensed under the Creative Commons Attribution license.

overall_design:
  A single human reference nephrectomy (female aged 59 without histologic evidence of kidney disease) was acquired from the Biopsy Biobank Cohort of Indiana (BBCI). From age-matched 8-10 week old 129/ SvEv mice (Taconic Biosciences, Albany, New York), tissues were acquired from a sham mouse in which the abdomen was opened and sutured back and mice which underwent ischemia-reperfusion injury (IRI) or cecal ligation and puncture (CLP). In the IRI model both renal pedicles were exposed and clamped for 22 minutes through a midline incision then released. In the CLP model, the cecum was ligated and punctured with a 25 gauge needle. Kidneys were excised upon sacrifice 6 hours after each procedure and frozen in Optimal Cutting Temperature (OCT) compound. Slide preparation (CG000240_Demonstrated_Protocol_VisiumSpatialProtocols_TissuePreparationGuide_Rev_A, 10X Genomics),  imaging  (CG000241_VisiumImagingGuidelinesTN_Rev_A, 10X Genomics), mRNA extraction, library preparation, and sequencing (CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics) were conducted according to Visium Spatial Gene Expression protocols . Frozen transverse 10 碌m sections from the human nephrectomy or each murine model were placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Tissue sections were fixed in methanol and stained with hematoxylin and eosin (H&E). Stained tissue sections were permeabilized for 12 minutes, and the cDNA libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 28bp+120bp paired-end sequencing mode.


dataset_id: STDS0000002
title: Spatiotemporal analysis of human intestinal development at single-cell resolution
species: Homo sapiens
tissues: Intestine
technologies: 10x Visium;scRNA
disease: Intestinal development
submission_date: 2020-09-28 00:00:00
last_modified: 2020-02-22 00:00:00
contacts: alison.simmons@ndm.ox.ac.uk
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158704
platforms: Illumina MiSeq;Illumina NextSeq 500;Illumina NovaSeq 6000
pmid: 33406409
has_paired: SCDS0000038
cell_types:
  epithelial;fibroblast;endothelial (EC);pericytes;neural (ENS);muscularis;mesothelium;myofibroblast;immune

summary:
  Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including novel epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe new functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders.

overall_design:
   Colon and terminal ileum tissue sections from 8-22 post-conceptual week fetal intestine samples were subject to single cell RNA-seq analysis.

contributors:
  FawknerCorbett D;Antanaviciute A;Parikh K;Jagielowicz M;Sousa Gerós A;Gupta T;Ashley N;Koohy H;Simmons A

citation:
  Fawkner-Corbett, David et al. “Spatiotemporal analysis of human intestinal development at single-cell resolution.” Cell vol. 184,3 (2021): 810-826.e23. doi:10.1016/j.cell.2020.12.016


dataset_id: STDS0000082
title: Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus
species: Mus musculus
tissues: Brain
organ_parts: Suprachiasmatic nucleus
development_stages: 8 weeks
technologies: Geo-seq
disease: Brain development
submission_date: 2018-08-10 00:00:00
last_modified: 2020-02-21 00:00:00
contributors: Meng Zhao
contacts: shaoangwen@live.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118403
platforms: GPL21273
pmid: 32066983
summary:
  We apply geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology, to investigate the heterogeneous nature of suprachiasmatic nucleus (SCN) in adult mouse. The 3D quantitative data enables spatial gene expression pattern visualization . The dataset identified genes that are coexpressed in a specific region, mark domains of similar global pattern of expression, and can be used for mapping the position of single cells dissociated from adult SCN.

overall_design:
  In laser capture microdissection (LCM), hexagon grids with 40-渭m maximal radius was used and the transcriptome of each hexagon was obtained using single-cell RNA-seq technology.

citation:
  Wen, Shao'ang et al. “Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus.” Nature neuroscience vol. 23,3 (2020): 456-467. doi:10.1038/s41593-020-0586-x


dataset_id: STDS0000099
title: RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus
species: Homo sapiens
tissues: Neuron
organ_parts: SHY neuroblasts
technologies: Proximity RNA-seq
disease: Neuron
overall_design: 4 Proximity RNA-Seq datasets (Pools 2, 5, 7 & 8), 2 Hi-C datasets
submission_date: 2019-04-12 00:00:00
last_modified: 2020-02-10 00:00:00
contacts: steven.wingett@babraham.ac.uk
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129732
platforms: GPL16791
pmid: 31992717;31267103
summary:
  Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing.

contributors:
  Morf J;Wingett SW;Farabella I;Cairns J;Furlan-Magaril M;Jiménez-García LF;Liu X;Craig FF;Walker S;Segonds-Pichon A;Andrews S;Marti-Renom MA;Fraser P

citation:
  Wingett, Steven W et al. “RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome.” Scientific data vol. 7,1 35. 28 Jan. 2020, doi:10.1038/s41597-020-0372-3


dataset_id: STDS0000083
title: Spatial Transcriptomics of Human Cardiac Tissue
species: Homo sapiens
tissues: Heart
technologies: Spatial Transcriptomics
disease: Heart failure
submission_date: 2019-08-14 00:00:00
last_modified: 2019-12-31 00:00:00
contributors: Olof Gidlöf;Gustav Smith
contacts: olof.gidlof@med.lu.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135805
platforms: GPL18573
pmid: 31862877
summary:
  Transplanted (healthy) and explanted human heart tissue sections (affected by different heart failure etiologies) were investigated for gene expression differences by using the Spatial Transcriptomics technology.

overall_design:
  Spatial transcriptomics analysis of biopsies from normal and hypertrophic, dilated and ischemic cardiomyopathy patients.

citation:
  Egerstedt, Anna et al. “Profiling of the plasma proteome across different stages of human heart failure.” Nature communications vol. 10,1 5830. 20 Dec. 2019, doi:10.1038/s41467-019-13306-y


dataset_id: STDS0000016
title: Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
species: Homo sapiens
tissues: Synovial
organ_parts: Synovial tissue
cell_types: T cell;B cell
technologies: Spatial Transcriptomics
disease: Rheumatoid arthritis (RA) and Spondyloarthritis (SpA)
submission_date: 2019-12-12 00:00:00
last_modified: 2019-12-12 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/doi-10-1038-s41598-019-55441-y/
pmid: 31831833
citation:
  Carlberg, Konstantin et al. “Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics.” Scientific reports vol. 9,1 18975. 12 Dec. 2019, doi:10.1038/s41598-019-55441-y


dataset_id: STDS0000015
title: A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
species: Homo sapiens
tissues: Embryo
organ_parts: Heart
development_stages: 4.5-5 PCW;6.5 PCW;9 PCW
technologies: Spatial Transcriptomics
disease: Heart development
submission_date: 2019-12-12 00:00:00
last_modified: 2019-12-12 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/doi-10-1016-j-cell-2019-11-025/
pmid: 31835037
has_paired: SCDS0000047
citation:
  Asp, Michaela et al. “A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.” Cell vol. 179,7 (2019): 1647-1660.e19. doi:10.1016/j.cell.2019.11.025


dataset_id: STDS0000063
species: Mus musculus
tissues: Colon
sex: Female
technologies: 10x Visium
disease: Colon development
submission_date: 2021-12-09 00:00:00
last_modified: 2019-12-11 00:00:00
contributors: Das S;Villablanca E;Larsson L
contacts: ludvig.larsson@scilifelab.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190595
platforms: Illumina NovaSeq 6000
pmid: 35149721
has_paired: STDS0000063
title:
  10x Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient/deficient mice

summary:
   The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10x Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon during mucosal healing upon dextran sodium sulfate (DSS) induced injury in mice in which B cell has been depleted and control.

overall_design:
  Female C57BL/6J mice were irradiated and received BM transplants with either CD19cre (ctrl) or CD19cre x iDTR cells. 8 weeks after BM transfer mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. On days 9, 10, 12 and 13 mice received i.p. injections of diphteria toxin (25ng/g BW) in PBS. On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for visium and submitted for sequencing.

citation:
  Parigi, Sara M et al. “The spatial transcriptomic landscape of the healing mouse intestine following damage.” Nature communications vol. 13,1 828. 11 Feb. 2022, doi:10.1038/s41467-022-28497-0


dataset_id: STDS0000064
title: High-definition spatial transcriptomics for in situ tissue profiling
species: Mus musculus
tissues: Brain
development_stages: 12 weeks
technologies: HDST
disease: Brain Cortex
overall_design: Three sections of the main olfactory bulb from adult C57BL/6J mice
submission_date: 2019-05-03 00:00:00
last_modified: 2019-09-20 00:00:00
contributors: Sanja Vickovic;Ludvig Bergenstråhle
contacts: vickovic@broadinstitute.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130682
platforms: Illumina NextSeq 500
pmid: 31501547
summary:
  Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.

citation:
  Vickovic, Sanja et al. “High-definition spatial transcriptomics for in situ tissue profiling.” Nature methods vol. 16,10 (2019): 987-990. doi:10.1038/s41592-019-0548-y


dataset_id: STDS0000135
title: LCM-Seq of niches and single-cell RNA-seq of mouse bone marrow
species: Mus musculus
tissues: Bone marrow
technologies: LCM-seq
disease: Bone marrow
summary: This SuperSeries is composed of the SubSeries listed below.
overall_design: Refer to individual Series
submission_date: 2018-11-13 00:00:00
last_modified: 2019-08-08 00:00:00
contacts: lars.velten@crg.eu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122467
platforms: GPL21103
cell_types:
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citation:
  Kurtova, Antonina V et al. “Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis.” Blood advances vol. 7,4 (2023): 491-507. doi:10.1182/bloodadvances.2022007714


dataset_id: STDS0000065
title: Atlas of Subcellular RNA Localization Revealed by APEX-Seq
species: Homo sapiens
technologies: APEX-seq
disease: Normal atlas
submission_date: 2018-06-19 00:00:00
last_modified: 2019-07-09 00:00:00
contacts: ffazal08@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116008
platforms: Illumina HiSeq 4000
pmid: 31230715
summary:
     We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

overall_design:
  APEX-seq libraries for both labeled targets and unlabeled controls were generated for the following constructs: (1) NLS (nucleus), (2) NIK (nucleolus), (3) LMA (nuclear lamina), (4) NucPore (nuclear pore), (5) NES (cytosol), (6) ERM (ER membrane cytosol facing), (7) KDEL (ER lumen), (8) OMM (Outer mitochondrial membrane), and (9) MITO (mitochondrial matrix). 4 libraries were prepared for each construct (2 biological replicates for labeled targets, 2 biological replicates for unlabeled controls). Furthermore, we generated drug-perturbation libraries for OMM and NES using the following treatments: (1) cycloheximide, (2) puromycin and (3) m-chlorophenylhydrazone (CCCP). In addition, nocodazole-perturbation libraries for OMM and NES were generated following drug treatment for: (1) 3 minutes, (2) 6 minutes, (3) 9 minutes, (4) 30 minutes and (5) 2 hours. We also generated nuclear and cytosol fractionation RNA-seq libraries (2 replicates each) following a protocol by Gagnon et al. (Nature Protocols, 2014).

contributors:
  Furqan M Fazal;Shuo Han;Kevin R Parker;Pornchai Kaewsapsak;Jin Xu;Alistair N Boettiger;Howard Y Chang;Alice Y Ting

citation:
  Fazal, Furqan M et al. “Atlas of Subcellular RNA Localization Revealed by APEX-Seq.” Cell vol. 178,2 (2019): 473-490.e26. doi:10.1016/j.cell.2019.05.027


dataset_id: STDS0000230
title: NIH3T3_point_locations for RNA seqFISH+ experiments
species: Mus musculus
tissues: Brain
organ_parts: Olfactory bulb;Cortex
technologies: seqFISH+
disease: Brain Cortex Olfactory bulb
submission_date: 2019-05-06 00:00:00
last_modified: 2019-05-06 00:00:00
accessions: https://zenodo.org/record/2669683
pmid: 30911168
summary:
  These source data consist of the point locations of individual decoded mRNA dots in seqFISH+ experiments on NIH/3T3 cells. DAPI_experiment folder contains the DAPI stainings with other beads images. ROIs_experiment folders are the manual segmentation performed in ImageJ. We only performed segmentation on the whole single cells. In seqFISH+_NIH3T3_point_locations zip folder, there are 3 matlab files . One is gene name file, the other two files are point locations for replicate 1 and 2 seqFISH+ experiments in NIH/3T3 cells. The columns of the data represent field of view(FOV), Cell , and Gene. For example : FOV1 , Cell 5, Gene : Bgn to retrieve the point locations. 

citation:
  Eng, Chee-Huat Linus et al. “Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.” Nature vol. 568,7751 (2019): 235-239. doi:10.1038/s41586-019-1049-y


dataset_id: STDS0000081
title: Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
species: Mus musculus
tissues: Spinal cord
development_stages: P70;P100;P120;P30
technologies: Spatial Transcriptomics
disease: Spin cord development
summary: Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
overall_design: 4 timepoints in SOD1-G93A model with WT control; 2 timepoints in ATG7 model
submission_date: 2018-09-24 00:00:00
last_modified: 2019-04-06 00:00:00
contributors: Sanja Vickovic
contacts: vickovic@broadinsitute.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120374
platforms: GPL21626
pmid: 30948552
citation:
  Maniatis, Silas et al. “Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.” Science (New York, N.Y.) vol. 364,6435 (2019): 89-93. doi:10.1126/science.aav9776


dataset_id: STDS0000232
title: Three-dimensional intact-tissue sequencing of single-cell transcriptional states
species: Mus musculus
tissues: Brain
organ_parts: Cortex
technologies: STARmap
disease: Brain Cortex
submission_date: 2019-01-21 00:00:00
last_modified: 2019-01-21 00:00:00
accessions: http://clarityresourcecenter.org
pmid: 29930089
citation:
  Wang, Xiao et al. “Three-dimensional intact-tissue sequencing of single-cell transcriptional states.” Science (New York, N.Y.) vol. 361,6400 (2018): eaat5691. doi:10.1126/science.aat5691


dataset_id: STDS0000079
species: Caenorhabditis elegans
sex: male
technologies: Tomo-seq
disease: Normal atlas
overall_design: Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections
submission_date: 2018-05-21 00:00:00
last_modified: 2018-11-05 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114723
platforms: GPL13657
pmid: 30416013
title:
  Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

summary:
  To advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used spatial | transcriptomics to generate high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region- and tissue-specific genes.  | We have found extensive sex-specific gene expression differences in the germline and sperm and discovered genes that are specifically expressed in the male reproductive tract. These include a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, enabling transcriptome-wide comparisons of gene expression patterns.

contributors:
  Annabel Ebbing;Abel Vertesy;Marco Betist;Bastiaan Spanjaard;Jan P Junker;Eugene Berezikov;Alexander van Oudenaarden;Hendrik C Korswagen

citation:
  Ebbing, Annabel et al. “Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns.” Developmental cell vol. 47,6 (2018): 801-813.e6. doi:10.1016/j.devcel.2018.10.016


dataset_id: STDS0000071
title: Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.
species: Mus musculus
tissues: Brain
technologies: MERFISH
disease: Normal atlas
submission_date: 2018-11-03 00:00:00
last_modified: 2018-11-03 00:00:00
contributors: Zhuang X;Dulac C
contacts: zhuang@chemistry.harvard.edu
pmid: 30385464
has_paired: STDS0000071
summary:
  The hypothalamus controls essential social behaviors and homeostatic functions. However, the cellular architecture of hypothalamic nuclei, including the molecular identity, spatial organization, and function of distinct cell types, is poorly understood. Here, we developed an imaging-based cell type identification and mapping method and combined it with single-cell RNA-sequencing to create a molecularly annotated and spatially resolved cell atlas of the mouse hypothalamic preoptic region. We profiled ~1 million cells, identified ~70 neuronal populations characterized by distinct neuromodulatory signatures and spatial organizations, and defined specific neuronal populations activated during key social behaviors in male and female mice, providing a high-resolution framework for mechanistic investigation of behavior circuits. The approach described here opens a new avenue for the construction of cell atlases in diverse tissues and organisms.

citation:
  Moffitt, Jeffrey R et al. “Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.” Science (New York, N.Y.) vol. 362,6416 (2018): eaau5324. doi:10.1126/science.aau5324

accessions:
  https://datadryad.org/stash/dataset/doi:10.5061/dryad.8t8s248;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113576


dataset_id: STDS0000054
species: Homo sapiens
tissues: Skin
technologies: Spatial Transcriptomics
disease: Cutaneous Malignant Melanoma
submission_date: 2018-08-28 00:00:00
last_modified: 2018-08-28 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/
pmid: 30154148
title:
  Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma

citation:
  Thrane, Kim et al. “Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.” Cancer research vol. 78,20 (2018): 5970-5979. doi:10.1158/0008-5472.CAN-18-0747


dataset_id: STDS0000053
title: Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
species: Homo sapiens
tissues: Prostate
technologies: Spatial Transcriptomics
disease: Prostate cancer
submission_date: 2018-06-20 00:00:00
last_modified: 2018-06-20 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/10-1038-s41467-018-04724-5/
pmid: 29925878
has_paired: SCDS0000017
citation:
  Berglund, Emelie et al. “Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.” Nature communications vol. 9,1 2419. 20 Jun. 2018, doi:10.1038/s41467-018-04724-5


dataset_id: STDS0000014
title: Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
species: Homo sapiens
tissues: Heart
organ_parts: Right atrial appendage (RAA);Left ventricular needle (LV)
development_stages: Adult
technologies: Spatial Transcriptomics
disease: Heart failure
submission_date: 2017-10-11 00:00:00
last_modified: 2017-10-11 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/doi10-1038s41598-017-13462-5/
pmid: 29021611
has_paired: SCDS0000047
citation:
  Asp, Michaela et al. “Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.” Scientific reports vol. 7,1 12941. 11 Oct. 2017, doi:10.1038/s41598-017-13462-5


dataset_id: STDS0000231
species: Mus musculus
tissues: Brain
organ_parts: Hippocampus
technologies: seqFish
disease: Brain Hippocampus
submission_date: 2017-10-09 00:00:00
last_modified: 2017-10-09 00:00:00
pmid: 27764670
title:
  In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus

citation:
  Shah, Sheel et al. “In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus.” Neuron vol. 92,2 (2016): 342-357. doi:10.1016/j.neuron.2016.10.001


dataset_id: STDS0000017
title: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
species: Mus musculus;Homo sapiens
tissues: Neuron
organ_parts: Olfactory bulb
technologies: Spatial Transcriptomics
disease: Olfactory bulb
submission_date: 2016-07-01 00:00:00
last_modified: 2016-07-01 00:00:00
accessions: https://www.spatialresearch.org/resources-published-datasets/doi-10-1126science-aaf2403/
pmid: 27365449
citation:
  Ståhl, Patrik L et al. “Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.” Science (New York, N.Y.) vol. 353,6294 (2016): 78-82. doi:10.1126/science.aaf2403


dataset_id: STDS0000237
title: Molecular and spatial signatures of mouse brain aging at single-cell resolution
species: Mus musculus
tissues: Brain
organ_parts: Frontal cortex; Striatum
development_stages: Junvenile; Young Adult;Old
technologies: MERFISH;snRNA
disease: Normal atlas
submission_date: 2022-07-13 00:00:00
last_modified: 2023-05-25 00:00:00
contributors: Allen WE, Blosser TR, Sullivan ZA, Dulac C, Zhuang X
contacts: weallen@fas.harvard.edu
accessions: https://cellxgene.cziscience.com/collections/31937775-0602-4e52-a799-b6acdd2bac2e
platforms: Illumina NovaSeq 6000
pmid: 36580914
has_paired: STDS0000237
summary:
  The diversity and complex organization of cells in the brain have hindered systematic characterization of age-related changes in its cellular and molecular architecture, limiting our ability to understand the mechanisms underlying its functional decline during aging. Here, we generated a high-resolution cell atlas of brain aging within the frontal cortex and striatum using spatially resolved single-cell transcriptomics and quantified changes in gene expression and spatial organization of major cell types in these regions over the mouse lifespan. We observed substantially more pronounced changes in cell state, gene expression, and spatial organization of non-neuronal cells over neurons. Our data revealed molecular and spatial signatures of glial and immune cell activation during aging, particularly enriched in the subcortical white matter, and identified both similarities and notable differences in cell-activation patterns induced by aging and systemic inflammatory challenge. These results provide critical insights into age-related decline and inflammation in the brain.

overall_design:
  Nuclei of 2 young (4 week old) and 2 aged (90 week old) mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence of Hoeschst signal and analyzed using 10X Genomics snRNA-seq.

citation:
  Allen WE, Blosser TR, Sullivan ZA, Dulac C et al. Molecular and spatial signatures of mouse brain aging at single-cell resolution. Cell 2023 Jan 5;186(1):194-208.e18.


dataset_id: SCDS0000001
title: Molecular architecture of the developing mouse brain
species: Mus musculus
tissues: Brain
sex: All
technologies: scRNA
disease: Normal atlas
submission_date: 2020-06-08 00:00:00
last_modified: 2020-06-08 00:00:00
contacts: Sweden. sten.linnarsson@ki.se
accessions: https://www.ncbi.nlm.nih.gov/sra?term=PRJNA637987
platforms: Illumina HiSeq 3000
pmid: 34321664
has_paired: STDS0000235
summary:
  The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell–cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characterization of cell states over the entire spatiotemporal range of brain development. The ability of single-cell RNA sequencing and spatial transcriptomics to reveal the molecular heterogeneity of complex tissues has therefore been particularly powerful in the nervous system. Previous studies have explored development in specific brain regions1,2,3,4,5,6,7,8, the whole adult brain9 and even entire embryos10. Here we report a comprehensive single-cell transcriptomic atlas of the embryonic mouse brain between gastrulation and birth. We identified almost eight hundred cellular states that describe a developmental program for the functional elements of the brain and its enclosing membranes, including the early neuroepithelium, region-specific secondary organizers, and both neurogenic and gliogenic progenitors. We also used in situ mRNA sequencing to map the spatial expression patterns of key developmental genes. Integrating the in situ data with our single-cell clusters revealed the precise spatial organization of neural progenitors during the patterning of the nervous system.

overall_design:
  Single-cell suspensions were prepared from microdissected tissue samples using enzymatic digestion followed by manual trituration. Cells were resuspended in artificial cerebrospinal fluid at 1000 cells/l and added to the reverse transcription mix aiming for 4000 cells. All downstream cDNA synthesis (12-13 PCR cycles), library preparation and sequencing were carried out according to the 10X Genomics Chromium Single Cell Kit Version 2.

contributors:
  Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Alejandro Mossi Albiach, Christoffer Mattsson Langseth, Irina Khven, Alex R. Lederer, Lisa M. Dratva, Anna Johnsson, Mats Nilsson, Peter Lönnerberg & Sten Linnarsson 

citation:
  La Manno, G., Siletti, K., Furlan, A. et al. Molecular architecture of the developing mouse brain. Nature 596, 92–96 (2021). https://doi.org/10.1038/s41586-021-03775-x


dataset_id: SCDS0000002
species: Homo sapiens
tissues: Skin
technologies: scRNA
disease: Atopic dermatitis
overall_design: Comparison of skin cells obtained by skin suction blistering and conventional biopsy
submission_date: 2020-06-03 00:00:00
last_modified: 2021-03-16 00:00:00
contacts: patrick.brunner@meduniwien.ac.at
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153760
platforms: Illumina HiSeq 3000
pmid: 32344053
has_paired: STDS0000212
title:
  Single-cell Transcriptomics Combined With Interstitial Fluid Proteomics Defines Cell Type-Specific Immune Regulation in Atopic Dermatitis

summary:
  Background: Atopic dermatitis (AD) is the most common chronic inflammatory skin disease, but its complex pathogenesis is only insufficiently understood, resulting in still limited treatment options.
  Objective: We sought to characterize AD on both transcriptomic and proteomic levels in humans.
  Methods: We used skin suction blistering, a painless and nonscarring procedure that can simultaneously sample skin cells and interstitial fluid. We then compared results with conventional biopsies.
  Results: Suction blistering captured epidermal and most immune cells equally well as biopsies, except for mast cells and nonmigratory CD163+ macrophages that were only present in biopsy isolates. Using single-cell RNA sequencing, we found comparable transcriptional profiles of key inflammatory pathways between blister and biopsy AD, but suction blistering was superior in cell-specific resolution for high-abundance transcripts (KRT1/KRT10, KRT16/KRT6A, S100A8/S100A9), which showed some background signals in biopsy isolates. Compared with healthy controls, we found characteristic upregulation of AD-typical cytokines such as IL13 and IL22 in Th2 and Th22 cells, respectively, but we also discovered these mediators in proliferating T cells and natural killer T cells, that also expressed the antimicrobial cytokine IL26. Overall, not T cells, but myeloid cells were most strongly enriched in AD, and we found dendritic cell (CLEC7A, amphiregulin/AREG, EREG) and macrophage products (CCL13) among the top upregulated proteins in AD blister fluid proteomic analyses.
  Conclusion: These data show that by using cutting-edge technology, suction blistering offers several advantages over conventional biopsies, including better transcriptomic resolution of skin cells, combined with proteomic information from interstitial fluid, unraveling novel inflammatory players that shape the cellular and proteomic microenvironment of AD.

contributors:
  Rojahn TB, Vorstandlechner V, Krausgruber T, Bauer WM, Alkon N, Bangert C, Thaler FM, Sadeghyar F, Fortelny N, Gernedl V, Rindler K, Elbe-Bürger A, Bock C, Mildner M, Brunner PM

citation:
  Rojahn TB, Vorstandlechner V, Krausgruber T, et al. Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type-specific immune regulation in atopic dermatitis. J Allergy Clin Immunol. 2020;146(5):1056-1069. doi:10.1016/j.jaci.2020.03.041


dataset_id: STDS0000238
title: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
species: Mus musculus
tissues: Brain
sex: Unknown
technologies: scRNA;MERFISH
disease: Normal atlas
contacts: cindy.vanvelthoven@alleninstitute.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE246717
platforms: Illumina NovaSeq 6000
pmid: 38092916
has_paired: STDS0000238
summary:
   	The mammalian brain consists of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled (~4.0 million cells passing quality control), and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into four nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present a newly developed online platform, Allen Brain Cell (ABC) Atlas, to visualize the mouse whole brain cell type taxonomy and atlas along with the scRNA-seq and MERFISH data and metadata sets. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate myriad modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cellular and circuit function, development, and evolution of the mammalian brain.

overall_design:
  Single cell RNA-seq using the 10x genomics v2 and v3 methods. Cells were isolated from whole mouse brain and each library represents a small dissection area. The dataset includes 299 10x genomics v2 libraries containing ~2.5 million cells and 482 10x genomics v3 libaries containing ~4.4 million cells.

contributors:
  Yao Z, van Velthoven CT, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Huang M, Hupp M, Jin K, Kroll M, Smith K, Zeng H

citation:
  Yao Z, van Velthoven CTJ, Kunst M, Zhang M et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023 Dec;624(7991):317-332.


dataset_id: SCDS0000003
species: Mus musculus
tissues: Muscle
organ_parts: Skeletal muscle (quadriceps)
technologies: snRNA
disease: Muscle regeneration
submission_date: 2020-08-19 00:00:00
last_modified: 2020-11-05 00:00:00
contributors: Francesco Chemello, Hui Li, John R. McAnally, Ning Liu, Rhonda Bassel-Duby, and Eric N. Olson
contacts: zhw063@health.ucsd.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156498
platforms: Illumina HiSeq 2500;Illumina NovaSeq 6000
pmid: 33148801
has_paired: STDS0000204
title:
  Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing

summary:
  Duchenne muscular dystrophy (DMD) is a fatal muscle disorder characterized by cycles of degeneration and regeneration of multinucleated myofibers and pathological activation of a variety of other muscle-associated cell types. The extent to which different nuclei within the shared cytoplasm of a myofiber may display transcriptional diversity and whether individual nuclei within a multinucleated myofiber might respond differentially to DMD pathogenesis is unknown. Similarly, the potential transcriptional diversity among nonmuscle cell types within dystrophic muscle has not been explored. Here, we describe the creation of a mouse model of DMD caused by deletion of exon 51 of the dystrophin gene, which represents a prevalent disease-causing mutation in humans. To understand the transcriptional abnormalities and heterogeneity associated with myofiber nuclei, as well as other mononucleated cell types that contribute to the muscle pathology associated with DMD, we performed single-nucleus transcriptomics of skeletal muscle of mice with dystrophin exon 51 deletion. Our results reveal distinctive and previously unrecognized myonuclear subtypes within dystrophic myofibers and uncover degenerative and regenerative transcriptional pathways underlying DMD pathogenesis. Our findings provide insights into the molecular underpinnings of DMD, controlled by the transcriptional activity of different types of muscle and nonmuscle nuclei.

overall_design:
  Transcriptome analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice; Single nucleus RNA-seq analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice.

citation:
  Chemello F, Wang Z, Li H, McAnally JR et al. Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencing. Proc Natl Acad Sci U S A 2020 Nov 24;117(47):29691-29701.


dataset_id: SCDS0000004
title: A human brain vascular atlas reveals diverse mediators of Alzheimer's risk
species: Homo sapiens
tissues: Brain
technologies: VINE-seq
disease: Alzheimer disease
submission_date: 2020-12-20 00:00:00
last_modified: 2022-12-09 00:00:00
contacts: andcyang@stanford.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163577
platforms: Illumina NovaSeq 6000
pmid: 35165441
has_paired: STDS0000189
summary:
  The human brain vasculature is of great medical importance: its dysfunction causes disability and death1, and the specialized structure it forms—the blood–brain barrier—impedes the treatment of nearly all brain disorders2,3. Yet so far, we have no molecular map of the human brain vasculature. Here we develop vessel isolation and nuclei extraction for sequencing (VINE-seq) to profile the major vascular and perivascular cell types of the human brain through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 9 individuals with Alzheimer’s disease and 8 individuals with no cognitive impairment. We identify brain-region- and species-enriched genes and pathways. We reveal molecular principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In Alzheimer’s disease, we observe selective vulnerability of ECM-maintaining pericytes and gene expression patterns that implicate dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 genes that have been linked to Alzheimer’s disease risk by genome-wide association studies (GWASs) are expressed in the human brain vasculature, and we confirm this by immunostaining. Vascular GWAS genes map to endothelial protein transport, adaptive immune and ECM pathways. Many are microglia-specific in mice, suggesting a partial evolutionary transfer of Alzheimer’s disease risk. Our work uncovers the molecular basis of the human brain vasculature, which will inform our understanding of overall brain health, disease and therapy.

overall_design:
  SIngle-cell profiling of hippocampus and superior frontal cortex from 25 hippocampus and cortex samples across 17 control and Alzheimer's disease (AD) patients

contributors:
  Andrew C Yang , Ryan T Vest , Fabian Kern, Davis P Lee , Maayan Agam, Christina A Maat , Patricia M Losada , Michelle B Chen , Nicholas Schaum , Nathalie Khoury , Angus Toland , Kruti Calcuttawala, Heather Shin , Róbert Pálovics, Andrew Shin, Elizabeth Y Wang, Jian Luo, David Gate, Walter J Schulz-Schaeffer, Pauline Chu, Julie A Siegenthaler, M Windy McNerney , Andreas Keller, Tony Wyss-Coray

citation:
  Yang, A.C., Vest, R.T., Kern, F. et al. A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk. Nature 603, 885–892 (2022). https://doi.org/10.1038/s41586-021-04369-3


