# datasets

dataset_id: SCDS0000005
title: Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer
species: Homo sapiens
tissues: Prostate
technologies: scRNA
disease: Prostatic cancer
submission_date: 2019-09-23 00:00:00
last_modified: 2023-09-08 00:00:00
contributors: Wang J, Gao W
contacts: wj860520@163.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137829
platforms: Illumina NovaSeq 6000
pmid: 35789834
has_paired: STDS0000227
summary:
  Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer, with a 10% five-year survival rate. However, little is known about its origin and the mechanisms governing its emergence. Our study characterized ADPC and NEPC in prostate tumors from 7 patients using scRNA-seq. First, we identified two NEPC gene expression signatures representing different phases of trans-differentiation. New marker genes we identified may be used for clinical diagnosis. Second, integrative analyses combining expression and subclonal architecture revealed different paths by which NEPC diverges from the original ADPC, either directly from treatment-naïve tumor cells or from specific intermediate states of treatment-resistance. Third, we inferred a hierarchical transcription factor (TF) network underlying the progression, which involves constitutive regulation by ASCL1, FOXA2, and selective regulation by NKX2-2, POU3F2, and SOX2. Together, these results defined the complex expression profiles and advanced our understanding of the genetic and transcriptomic mechanisms leading to NEPC differentiation.

overall_design:
  Single cell mRNA profiles of 6CRPC patients were generated by 10X Genomics platform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)

citation:
  Wang Z, Wang T, Hong D, et al. Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer. iScience. 2022;25(7):104576. Published 2022 Jun 13. doi:10.1016/j.isci.2022.104576


dataset_id: SCDS0000006
species: Homo sapiens
tissues: Liver
technologies: scRNA
disease: colorectal cancer
submission_date: 2021-06-16 00:00:00
last_modified: 2021-09-20 00:00:00
contributors: Li J, Che L
contacts: cheliheng@126.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178318
platforms: Illumina NovaSeq 6000
pmid: 34489408
has_paired: STDS0000219
title:
  A Single-Cell Atlas of Liver Metastases of Colorectal Cancer Reveals the Reprogramming of the Tumor Microenvironment in Response to Preoperative Chemotherapy

summary:
  Metastasis is the primary cause of cancer-related mortality in colorectal cancer (CRC) patients. How to improve therapeutic options for patients with metastatic CRC (mCRC) is the core question for CRC treatment. However, the complexity and diversity of stromal context of the tumor microenvironment (TME) in liver metastases of CRC is not fully understood, and its influence on response to chemotherapy is unclear. Here we provide an in-depth analysis of transcriptional landscape of primary CRC, matched liver metastases and blood at single-cell resolution, and perform a systematic examination of transcriptional changes and phenotypic alteration of the TME in response to preoperative chemotherapy (PC). Based on 111,292 single-cell transcriptomes, our study reveals that TME of treatment-naïve tumors is characterized by higher abundance of less-activated B cells and higher heterogeneity of tumor-associated macrophages (TAMs). By contrast, in tumors treated with PC, we find activation of B cells, lower diversity of TAMs with immature and less activated phenotype, lower abundance of both dysfunctional T cells and ECM-remodeling cancer-associated fibroblasts (CAFs), and an accumulation of myofibroblasts. Our study provides a foundation for future investigation of the cellular mechanisms underlying liver metastasis of CRC and its response to PC, and opens up new possibilities for the development of therapeutic strategies for CRC.

overall_design:
  Single-cell expression profiling of the liver metastases of CRC in treatment patients and untreated patients.
  For data usage terms and conditions, please contact the principle investigator (Jianming Li, pathologylee@126.com).

citation:
  Che LH, Liu JW, Huo JP, Luo R et al. A single-cell atlas of liver metastases of colorectal cancer reveals reprogramming of the tumor microenvironment in response to preoperative chemotherapy. Cell Discov 2021 Sep 7;7(1):80.


dataset_id: SCDS0000007
title: Exploring the human lacrimal gland using organoids and single-cell sequencing
species: Homo sapiens
tissues: Eye
organ_parts: Adenoid cystic carcinoma of lacrimal gland
technologies: scRNA
disease: Normal atlas
submission_date: 2021-01-07 00:00:00
last_modified: 2021-03-30 00:00:00
contacts: m.bannier@hubrecht.eu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164403
platforms: Illumina NextSeq 500
pmid: 33730555
has_paired: STDS0000221
summary:
  The lacrimal gland is essential for lubrication and protection of the eye. Disruption of lacrimal fluid production, composition, or release results in dry eye, causing discomfort and damage to the ocular surface. Here, we describe the establishment of long-term 3D organoid culture conditions for mouse and human lacrimal gland. Organoids can be expanded over multiple months and recapitulate morphological and transcriptional features of lacrimal ducts. CRISPR-Cas9-mediated genome editing reveals the master regulator for eye development Pax6 to be required for differentiation of adult lacrimal gland cells. We address cellular heterogeneity of the lacrimal gland by providing a single-cell atlas of human lacrimal gland tissue and organoids. Finally, human lacrimal gland organoids phenocopy the process of tear secretion in response to neurotransmitters and can engraft and produce mature tear products upon orthotopic transplantation in mouse. Together, this study provides an experimental platform to study the (patho-)physiology of the lacrimal gland.

overall_design:
  Human lacrimal gland tissue was obtained from the UMC Utrecht. Tissue was dissociated into single-cell and stained for EpCAM, NGFR or nothing. Then cells were sorted into plates. For human organoids, cells were cultured in expansion medium for 7 or 9 days and, to differentiate them, they were first split into expansion medium for 2 days then switched to differentiation medium for 7 days, as described before. Then, organoids were dissociated and FAC sorted.

contributors:
  Bannier-Hélaouët M, Post Y, Korving J, Trani Bustos M, Gehart H, Beghtel H, Bar-Ephraim YE, van der Vaart J, Kalmann R, Imhoff SM, Clevers H

citation:
  Bannier-Hélaouët M, Post Y, Korving J, Trani Bustos M et al. Exploring the human lacrimal gland using organoids and single-cell sequencing. Cell Stem Cell 2021 Jul 1;28(7):1221-1232.e7.


dataset_id: SCDS0000010
title: Mapping the mouse developmental and aging atlas by single cell mRNA-seq
species: Mus musculus
tissues: Ovarian
sex: Unknown
technologies: scRNA
disease: Normal atlas
contributors: Guo G, Han X, Wang R, Sun H
contacts: ggj@zju.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108097
platforms: HiSeq X Ten
pmid: 35929025
has_paired: STDS0000162
summary:
  Single-cell mRNA sequencing (mRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built a comprehensive mouse cell atlas to catalog all cell types by collecting scRNA-seq data in the fetal and adult stages. Howerver, systematically study for organism-level dynamic changes of cellular states across mouse life span are still lacking. Here, We made an updated version of mouse cell atlas (MCA) by adding scRNA-seq data covering 14 major mouse organs during different mouse development period. We revealed aging related regulatory networks and pathways that have not been well characterized previously. We found that the expressions of immune-related genes, such as antigen-presenting genes and immunoglobulin genes, appeared in non-immune cell types in aging process. We also focused on the expression of lung epithelial immunoglobulin genes and revealed their related transcriptional regulation mechanisms. The updated MCA resource provides a valuable resource for studying mammalian development, maturation and aging.

overall_design:
  Microwell datasets for ten mouse tissues (brain, heart, intestine, kidney, liver, lung, pancreas, stomach, testis and uterus) covering 8 stages including E14.5, neonatal, 10d, 3w, 6-8w, 12m, 18m and 24m, four mouse tissues (bladder, spleen and prostate) covering aging stages including 6-8w, 12m, 18m, 24m, one tissue (thymus) covering aging stages including 6-8w, 12m, 18m and some mouse tissues used in GSE134355 and GSE108097.

citation:
  Wang R, Zhang P, Wang J, Ma L et al. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res 2023 Jan 25;51(2):501-516. 


dataset_id: SCDS0000011
title: Altered oligodendrocyte heterogeneity in Multiple sclerosis.
species: Homo sapiens
tissues: Brain
sex: Unknown
technologies: scRNA
disease: Embryonic brain
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118257
platforms: Illumina HiSeq 2500
pmid: 30747918
has_paired: STDS0000224
summary:
  Oligodendrocyte (OL) pathology is increasingly implicated in neurodegenerative diseases, as they are involved in metabolic support of axons and functional cross-talk with other brain cells. Rodent OLs are heterogeneous, with developmental and biological differences, but the extent of heterogeneity in the normal human brain and its contribution to any changes of disease remains unknown. Here we performed single nuclei RNA-sequencing (snRNA-seq) from white matter (WM) areas of post mortem human brain both in control (Ctr) and multiple sclerosis (MS) patients. We identified several sub-clusters of oligodendroglia in the Ctr human WM, some similar to those in mouse, and defined new markers for these. Strikingly, some of these sub-clusters were under-represented in MS tissue, while others were more prevalent than in controls. There was a lack of OL precursor cells (OPCs) and OLs in an intermediate stage of differentiation in MS lesions and in normal appearing white matter (NAWM), suggesting either depletion by the disease or by a regenerative response. The differences in mature OL sub-clusters indicate different functional states of OLs in MS tissue and, as this is similar in NAWM to lesions, that MS is a more diffuse brain disease than the focal demyelinating lesions suggest. We were also able to identify new markers of different MS lesion subtypes. Our findings of an altered heterogeneity of oligodendroglia in MS may have an important contribution to our understanding of disease progression and may alter therapeutic approaches to MS.

overall_design:
  We isolated single nuclei from white matter post-mortem tissue from 5 non-neurological control samples (Ctrl) and post-mortem tissue from 4 progressive Multiple sclerosis (MS) patients. We got a total of 20 samples, which in the MS samples included different non-lesioned (normal appearing white matter) and lesioned (active lesions, chronic active lesions, chronic inactive lesions and remyelinating lesions) based on pathology, to address the cellular and functional differences between the two groups.

contributors:
  Jäkel S, Agirre E, Falcao AM, van Bruggen D, Lee KW, Knuesel I, Malhotra D, ffrench-Constant C, Williams A, Castelo-Branco G

citation:
  Jäkel S, Agirre E, Mendanha Falcão A, van Bruggen D et al. Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature 2019 Feb;566(7745):543-547.


dataset_id: SCDS0000012
species: Homo sapiens
tissues: Kidney
sex: Unknown
technologies: scRNA
disease: Kidney cancer
contacts: twu@gene.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139555
platforms: Illumina HiSeq 4000
pmid: 32103181
has_paired: STDS0000223
title:
  Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy

summary:
  We performed single-cell RNA sequencing (scRNA-seq) and deep analysis of T cell receptor (TCR) clonotypes (scTCR-seq) in cancer patients across several indications, assessing the profiles of TCRs in the various populations of T cells in tumours, normal adjacent tissue (NAT), and peripheral blood. In a subset of patients, we find clear evidence of clonotypic expansion of T effector-like cells not only within the tumour but also in NAT.

overall_design:
  Single-cell RNA-seq and single-cell TCR-seq of pretreatment samples from 14 cancer patients, taken from tumor, normal adjacent tissue, and peripheral blood

contributors:
  Wu TD, Madireddi S, de Almeida PE, Banchereau R, Chen YJ, Chitre AS, Chiang EY, Iftikhar H, O'Gorman WE, Au-Yeung A, Takahashi C, Goldstein LD, Poon C, Keerthivasan S, de Almeida Nagata DE, Du X, Lee H, Banta KL, Mariathasan S, Das Thakur M, Huseni M, Ballinger M, Estay I, Caplazi P, Modrusan Z, Delamarre L, Mellman I, Bourgon R, Grogan JL

citation:
  Wu TD, Madireddi S, de Almeida PE, Banchereau R et al. Peripheral T cell expansion predicts tumour infiltration and clinical response. Nature 2020 Mar;579(7798):274-278.


dataset_id: SCDS0000013
species: Mus musculus
tissues: Lung
sex: Unknown
technologies: scRNA
disease: Lung cancer
contacts: rapolas.zilionis@bti.vu.lt
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127465
platforms: Illumina NextSeq 500
pmid: 30979687
has_paired: STDS0000129
title:
  Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species

summary:
  Tumor-infiltrating myeloid cells (TIMs) comprise monocytes, macrophages, dendritic cells and neutrophils, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map TIMs in non-small cell lung cancer patients. We uncovered 25 TIM states, most of which were reproducibly found across patients. To facilitate translational research of these populations, we also profiled TIMs in mice. In comparing TIMs across species, we identified a near-complete congruence of population structures among dendritic cells and monocytes; conserved neutrophil subsets; and species differences among macrophages. By contrast, myeloid cell population structures in patients’ blood showed limited overlap with those of TIMs. This study determines the lung TIM landscape and sets the stage for future investigations into the potential of TIMs as immunotherapy targets.

overall_design:
  Single cell RNA sequencing (scRNAseq) of RBC-depleted cells from non-small cell lung tumor and from blood of 7 patients. ScRNAseq of CD45-positive cells from lungs of 2 healthy mice and 2 lung tumor-bearing mice.

contributors:
  Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, Krishnan I, Maroni G, Meyerovitz CV, Kerwin CM, Choi S, Richards WG, De Rienzo A, Tenen DG, Bueno R, Levantini E, Pittet MJ, Klein AM

citation:
  Zilionis R, Engblom C, Pfirschke C, Savova V et al. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity 2019 May 21;50(5):1317-1334.e10. 


dataset_id: SCDS0000014
title: Dissecting the genetic and microenvironmental factors of gastric tumorigenesis in mice
species: Mus musculus
tissues: Stomach
organ_parts: Gastric cancer
sex: Unknown
technologies: scRNA
disease: Gastric cancer
overall_design: Gastric tumorigenesis in mice
contributors: Lu Z, Zhong A, Liu H, Chen C
contacts: irenezhongailing@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188761
platforms: Illumina NovaSeq 6000
pmid: 36261019
has_paired: STDS0000093
summary:
  Gastric cancer (GC) is one of the most frequent and lethal malignancies in the world. However, our understanding of the mechanisms underlying its initiation and progression is limited. Here, we applied genome-edited gastric organoids to establish a series of primary GC models in mice, which elucidated the genetic drivers for sequential transformation from dysplasia to well-differentiated and poorly differentiated GC. Further, we found that the orthotopic GC, but not the subcutaneous GC even with the same genetic drivers, displayed remote metastasis, suggesting critical roles of the microenvironment in GC metastasis. Through single-cell RNA-seq analyses and functional studies, we revealed that the molecular interaction between fibronectin 1 on stomach-specific macrophages and integrin α6β4 on GC cells promoted liver metastasis. Taken together, our studies proposed a new strategy to model GC and dissected the genetic and microenvironmental factors driving the full-range gastric tumorigenesis.

citation:
  Lu Z, Zhong A, Liu H, Zhang M et al. Dissecting the genetic and microenvironmental factors of gastric tumorigenesis in mice. Cell Rep 2022 Oct 18;41(3):111482.


dataset_id: SCDS0000015
species: Mus musculus
tissues: Heart
sex: Unknown
technologies: scRNA
disease: Heart failure
contributors: Ju Chen
contacts: juchen@health.ucsd.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179393
platforms: Illumina HiSeq 4000
pmid: 34915728
has_paired: STDS0000124
title:
  PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle

summary:
  Tissue samples were digested with 0.25% trypsin and gently dispersed into single-cell suspension with pipetting. Cells were filtered with a 40 μm cell strainer and subjected to fluorescence-activated cell sorting (FACS) to select for live cardiomyocytes which had positive tdTomato fluorescence and negative DAPI staining. Sorted live cardiomyocytes were then captured with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics) following manufacturer’s instructions.
  Single cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) using Chromium Next GEM Chip G in the chromium controller. Immediately following GEM generation, the Gel Bead was dissolved, primers were released, and co-partitioned cell was lysed, and its mRNA were reverse transcribed into barcoded cDNA. After further cleanup and amplification, the cDNA was enzymatically fragmented and amplified via PCR to generate sufficient mass for library construction. After end repair, A-tailing, adaptor ligation and sample index PCR, the library comprised constructs containing the sample index, UMI sequences, barcode sequences, and Illumina standard sequencing primers P5 and P7 at both ends.

overall_design:
  Single cell transcriptomic reads were processed using cellranger (version: 4.0.0)
  Further analysis was performed using Seurat (version: 3.2.0) on high quality cells with less than twenty percent of mitochondrial contaminations and larger than 2500 measured genes.
  To sufficiently separate cell populations, high resolution graph-based clustering was carried out on 30 principal components followed by UMAP dimension reduction, generating 53 subclusters.
  Genome_build: mm10
  Supplementary_files_format_and_content: features and barcodes in TSV and matrix in MTX generated by 10x Genomics software

citation:
  Wu T, Liang Z, Zhang Z, Liu C et al. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle. Circulation 2022 Feb 22;145(8):586-602.


dataset_id: SCDS0000016
title: Single-cell RNA-seq of mouse cerebral cortex
species: Mus musculus
tissues: Brain
sex: Unknown
technologies: scRNA
disease: Normal atlas
contributors: Zeisel A, Muñoz Manchado AB, Lönnerberg P, Linnarsson S
contacts: sten.linnarsson@ki.se
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60361
platforms: Illumina HiSeq 2000
pmid: 28729663
has_paired: STDS0000019
summary:
  We have applied a recently developed, highly accurate and sensitive single-cell RNA-seq method (STRT/C1) to perform a molecular census of two regions of the mouse cerebral cortex: the somatosensory cortex and hippocampus CA1.

overall_design:
  We isolated cells fresh from somatosensory cortex (S1) and hippocampus CA1 area of juvenile (P22 - P32) CD1 mice, 33 males and 34 females. Cells were collected without selection, except that 116 cells were obtained by FACS from 5HT3a-BACEGFP transgenic mice. A total of 76 Fluidigm C1 runs were performed, each attempting 96 cell captures and resulting in 3005 high-quality single-cell cDNAs, containing Unique Molecular Identifiers allowing counting of individual mRNA molecules, even after PCR amplification.

citation:
  Zeisel A, Muñoz-Manchado AB, Codeluppi S, Lönnerberg P et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 2015 Mar 6;347(6226):1138-42


dataset_id: SCDS0000008
species: Mus musculus
tissues: Brain
sex: Unknown
technologies: scRNA
disease: Brain injury
submission_date: 2020-11-03 00:00:00
last_modified: 2021-02-15 00:00:00
contributors: Witcher KG, Godbout JP
contacts: kristina.witcher@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE160763
platforms: Illumina HiSeq 2000
pmid: 36825001
has_paired: STDS0000201
title:
  Traumatic Brain Injury Causes Chronic Cortical Inflammation and Neuronal Dysfunction Mediated by Microglia

summary:
  Traumatic brain injury (TBI) can lead to significant neuropsychiatric problemsand neurodegenerative pathologies, which develop and persist years after injury. Neuroinflammatory processes evolve over this same period. Cortical mRNA analysis showed a robust contribution of microglia to neuroinflammatory pathways that persisted over time post-injury. These data also indicate that inflammation persists in the subacute and chronic time points after TBI, which may affect surrounding neurons, oligodendrocytes and astrocytes. To investigate this hypothesis, a single-cell sequencing approach was used to determine cell-type specific gene expression within the cortex 7 dpi with and without microglial depletion.

overall_design:
  Mice were subjected to midline fluid percussion injury (TBI) or kept as naïve controls. Half of the mice were fed PLX5622 (colony stimulating factor 1-receptor antagonist) in the chow prior to injury and up until the 7 dpi endpoint; the other half were fed AIN-7 vehicle chow. PLX5622 and CSF1R antagonism were used to deplete microglia. Therefore there were four experimental groups: Control, Control+PLX5622, TBI, and TBI+PLX5622. Cortex was dissociated and single cell suspensions from 3 mice per group were pooled into a single sample. This experiment was completed in two replicates (6 mice per group total; 2 experimental replicates per group).

citation:
  Witcher KG, Bray CE, Chunchai T, Zhao F et al. Traumatic Brain Injury Causes Chronic Cortical Inflammation and Neuronal Dysfunction Mediated by Microglia. J Neurosci 2021 Feb 17;41(7):1597-1616.


dataset_id: SCDS0000017
species: Homo sapiens
tissues: Prostate
sex: Unknown
technologies: scRNA
disease: Prostatic cancer
contributors: Song H, Weinstein HN, Allegakoen P, Wadsworth II MH, Xie J, Yang H, Huang FW
contacts: angelussong@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176031
platforms: Illumina HiSeq 2000
pmid: 35013146
has_paired: STDS0000116
title:
  Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

summary:
  Methods: To characterize the prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients.
  Results: We identify a population of tumor-associated club cells that could be associated with prostate carcinogenesis and uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer. ERG- tumor cells, compared to ERG+ cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids recapitulate tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues.
  Conclusions:Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

overall_design:
  Single-cell RNA sequencing based on Seq-Well S^3 protocol of 6 prostate biopsies from 3 different patients, 4 radical prostatectomies with tumor-only samples from 4 patients, and 4 radical prostatectomies with matched normal samples from 4 patients. Organoids derived from radical prostatectomy paired tumor and normal tissue samples.

citation:
  Song H, Weinstein HNW, Allegakoen P, Wadsworth MH 2nd et al. Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states. Nat Commun 2022 Jan 10;13(1):141. 


dataset_id: SCDS0000018
title: A single-cell and spatially resolved atlas of human breast cancers
species: Homo sapiens
tissues: Breast
organ_parts: Breast cancer
sex: Female
technologies: scRNA
disease: Breast cancer
submission_date: 2021-01-03 00:00:00
last_modified: 2021-02-15 00:00:00
contributors: Swarbrick A, Wu S, Al-Eryani G, Roden D
contacts: a.swarbrick@garvan.org.au
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176078
platforms: Illumina NextSeq 500
pmid: 34493872
has_paired: STDS0000239
summary:
  This study presents a single cell and spatially resolved transcriptomics analysis of human breast cancers. We develop a single cell method of intrinsic subtype classification (scSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using CITE-Seq provides high-resolution immune profiles, including novel PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell surface protein expression through differentiation within 3 major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into anti-tumor immune regulation. Using single cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed ‘ecotypes’, with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.

overall_design:
  We performed scRNA-Seq (Chromium, 10X Genomics) on 26 primary tumors from three major clinical subtypes of breast cancer, including 11 ER+, 5 HER2+ and 10 TNBC. We also performed bulk RNA-Seq on a total of 24 of these matched samples.

citation:
  Wu SZ, Al-Eryani G, Roden DL, Junankar S et al. A single-cell and spatially resolved atlas of human breast cancers. Nat Genet 2021 Sep;53(9):1334-1347. 


dataset_id: STDS0000241
title: Interleukin-17 governs hypoxic adaptation of injured epithelium
species: Mus musculus
tissues: Skin
sex: Unknown
technologies: 10x Visium; RNA-seq;CITE-seq
disease: Epithelium injury
submission_date: 2021-02-17 00:00:00
last_modified: 2023-01-05 00:00:00
contributors: Konieczny P, Yue X, Sidhu I, Naik S
contacts: Shruti.Naik@nyulangone.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166950
platforms: Illumina NovaSeq 6000;Illumina HiSeq 4000
pmid: 35709248
has_paired: STDS0000241
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 P, Xing Y, Sidhu I, Subudhi I et al. Interleukin-17 governs hypoxic adaptation of injured epithelium. Science 2022 Jul 8;377(6602):eabg9302. 


dataset_id: STDS0000242
species: Mus musculus
tissues: Bone
sex: Unknown
technologies: 10x Visium
disease: Bone marrow
submission_date: 2021-05-12 00:00:00
last_modified: 2021-12-29 00:00:00
contributors: Clemens TL, James AW, Tower RJ
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174313
platforms: Illumina HiSeq 2000
pmid: 34663698
has_paired: SCDS0000020
title:
  Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGFβ 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 TGFβ 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/TGFβ 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/TGFβ 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 RJ, Li Z, Cheng YH, Wang XW et al. Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling. Proc Natl Acad Sci U S A 2021 Oct 19;118(42). 


dataset_id: SCDS0000020
title: Single cell transcriptomics analysis of bone marrow mesenchymal lineage cells
species: Mus musculus
tissues: Bone
sex: Unknown
technologies: scRNA
disease: Bone marrow
submission_date: 2021-02-18 00:00:00
last_modified: 2022-05-11 00:00:00
contacts: ltyao@cmu.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145477
platforms: Illumina HiSeq 3000
pmid: 32286228
has_paired: STDS0000242
summary:
  Bone marrow mesenchymal lineage cells are a heterogeneous cell population involved in bone homeostasis and diseases such as osteoporosis. While it is long postulated that they originate from mesenchymal stem cells (MSCs), the true identity of MSCs and their in vivo bifurcated differentiation routes into osteoblasts and adipocytes remain poorly understood. Here, by employing large scale single cell transcriptome analysis, we computationally defined MSCs and delineated their bi-lineage differentiation paths in young, adult and aging mice. One identified subpopulation is a unique cell type that expresses adipocyte markers but contains no lipid droplets. As non-proliferative precursors for adipocytes, they exist abundantly as pericytes and stromal cells that form a ubiquitous 3D network inside the marrow cavity. Functionally they play critical roles in maintaining marrow vasculature and suppressing bone formation. Therefore, we name them marrow adipogenic lineage precursors (MALPs) and conclude that they are a new component of marrow adipose tissue.

overall_design:
  4 batches of single cell libraries for sequencing: endosteal Td+ bone marrow cells from 1-month-old (n=2), 1.5-month-old (n=3), 3-month-old (n=3) and 16-month-old (n=3) male Col2/Td mice. 20,000 cells were loaded in aim of acquiring one single library of 10,000 cell for each age group by Chromium controller (V3 chemistry version, 10X Genomics Inc, San Francisco, USA), barcoded and purified as described by the manufacturer, and sequenced using a 2x150 pair-end configuration on an Illumina HiSeq platform at a sequencing depth of ~400 million reads.

contributors:
  Zhong L, Yao L, Tower RJ, Wei Y, Miao Z, Park J, Shrestha R, Wang L, Yu W, Holdreith N, Zhang Y, Tong W, Gong Y, Ahn J, Susztak K, Dyment N, Li M, Long F, Chen C, Seale P, Qin L

citation:
  Zhong L, Yao L, Tower RJ, Wei Y et al. Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment. Elife 2020 Apr 14;9. 


dataset_id: STDS0000243
title: Integrated spatial multi-omics reveals fibroblast fate during tissue repair
species: Mus musculus
tissues: Skin
sex: Unknown
technologies: scRNA;10x Visium;RNA-seq;scATAC-seq
disease: Tissue repair
submission_date: 2021-01-23 00:00:00
last_modified: 2022-11-29 00:00:00
contributors: Januszyk M, Foster DS
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178758
platforms: Illumina HiSeq 2000;Illumina NextSeq 500
pmid: 34620713
has_paired: STDS0000243
summary:
  In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing across both time and space. We employ a stented wound model that recapitulates human tissue repair kinetics and multiple Rainbow transgenic lines to precisely track fibroblast fate during the physiologic response to injury. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to define the mechanisms controlling cell fate during migration, proliferation, and differentiation following tissue injury and thereby reexamine the canonical phases of wound healing. We show that wounding triggers a polyclonal proliferation of tissue-resident, mechano-responsive fibroblasts, the subpopulations of which inhabit spatially-distinct regions within the wound and harbor distinct activities. These findings have broad implications for the study of tissue repair in complex organ systems.

overall_design:
  Mouse wound tissue transcriptomes were profiles using RNA bulk and single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For bulk RNA sequencing, RNA was obtained from mouse inner wound region and outer wound region, as well as uninjured control fibroblasts at post-operative day (POD) #7 and #14, as well as inner wound region and outer wound region fibroblasts from POD #14 treated with a small molecule FAK inhibitor. For single-cell RNA sequencing, FACS-isolated Rainbow mouse inner wound region and outer wound region fibroblasts harvested at 3 timepoints over the course of wound healing (POD #2, #7, and #14) and single cell sorted for plate-seq. For single-cell ATAC sequencing, Rainbow mouse wound fibroblasts were FACS-isolated from inner and outer wound regions at the same 3 timepoints as single-cell RNA sequencing. For Visium spatial transcriptomics, mouse wound tissue sections were mounted and sequenced from POD #2, #7, and #14 as well as uninjured skin.

citation:
  Foster DS, Januszyk M, Yost KE, Chinta MS et al. Integrated spatial multiomics reveals fibroblast fate during tissue repair. Proc Natl Acad Sci U S A 2021 Oct 12;118(41).


dataset_id: STDS0000244
title: Spatial transcriptomics of human brain metastases
species: Homo sapiens
tissues: Brain
sex: Unknown
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: 2022-06-27 00:00:00
contributors: Hudson WH
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179572
platforms: Illumina NovaSeq 6000
pmid: 35584630
has_paired: SCDS0000021
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 μM 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:
  Sudmeier LJ, Hoang KB, Nduom EK, Wieland A et al. Distinct phenotypic states and spatial distribution of CD8(+) T cell clonotypes in human brain metastases. Cell Rep Med 2022 May 17;3(5):100620.


dataset_id: SCDS0000021
title: Single cell RNA-sequencing of human brain metastasis-infiltrating T cells
species: Homo sapiens
tissues: Brain
sex: Unknown
technologies: scRNA
disease: brain metastases cancer
summary: The goal of this study is to understand the biology of brain metastasis-infiltrating T cells.
submission_date: 2021-07-03 00:00:00
last_modified: 2022-06-27 00:00:00
contributors: Hudson WH
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179373
platforms: Illumina NovaSeq 6000
pmid: 35584630
has_paired: STDS0000244
overall_design:
  Single cell suspensions were generated from surgically-resected metastatic brain tumors. For five patients (5, 14, 15, 16, and 17), tumor-infiltrating PD-1+ CD8 T cells were isolated by FACS from each patient, combined with patient-matched circulating naive CD8 T cells and subjected to scRNA-seq with VDJ sequencing. Hashing antibodies were used to distinguish naïve (Totalseq C0251) from tumor-infiltrating (Totalseq C0252) cells. Separate captures and sequencing libraries were generated for each patient. An additional scRNA-seq experiment was performed on pooled tumor-infiltrating total (CD4 + CD8) T cells from patient 16 (Totalseq C0251), patient 26 (Totalseq C0252), and patient 27 (Totalseq C0253). Circulating T cells were also sorted from a healthy donor and included with this experiment (Totalseq C0254). Cells were pooled, two captures were performed, and libraries were sequenced. In this latter experiment, cells were also stained with anti-CD8 Totalseq C0046, anti-CD4 Totalseq C0045, and anti-PD-1 biotin followed by streptavidin Totalseq C0961.
  Please note that each processed data was generated from GEX, CITE-seq, and VDJ libraries, and is linked to the corresponding GEX sample records

citation:
  Sudmeier LJ, Hoang KB, Nduom EK, Wieland A et al. Distinct phenotypic states and spatial distribution of CD8(+) T cell clonotypes in human brain metastases. Cell Rep Med 2022 May 17;3(5):100620.


dataset_id: STDS0000245
species: Mus musculus
tissues: Blastema
sex: Unknown
technologies: 10x Visium
disease: Digit Regeneration
submission_date: 2021-07-22 00:00:00
last_modified: 2022-06-02 00:00:00
contributors: Sammarco MC, Tower RJ
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180682
platforms: Illumina HiSeq 2000;Illumina HiSeq 2500
pmid: 35616636
has_paired: SCDS0000022
title:
  Spatial transcriptomics reveals increased energetic requirements underpinning age-dependent declines in digit regeneration rescued through administration of OAA

summary:
  De novo limb regeneration after amputation is restricted in mammals to the distal digit tip. Central to this regenerative process is the blastema, a heterogeneous population of lineage-restricted, dedifferentiated cells that ultimately orchestrates the regeneration of the amputated bone and surrounding soft tissue. To investigate skeletal regeneration, we made use of spatial transcriptomics to characterize the transcriptional profile specifically within the blastema. Using this technique, we generated a gene signature with high specificity for the blastema in both our spatial data, as well as other previously published single-cell RNA-sequencing transcriptomic studies. To elucidate potential mechanisms distinguishing regenerative from non-regenerative healing, we applied spatial transcriptomics to an aging model. Consistent with other forms of repair, our digit amputation mouse model showed a significant impairment in regeneration in aged mice. Contrasting young and aged mice, spatial analysis revealed a metabolic shift in aged blastema associated with an increased bioenergetic requirement. This enhanced metabolic turnover was associated with increased hypoxia and angiogenic signaling, leading to excessive vascularization and altered regenerated bone architecture in aged mice. Restoration of this metabolic deficiency using the metabolite oxaloacetate enhanced in vivo bone regeneration. Thus, targeting cell metabolism may be a promising strategy to mitigate aging-induced declines in tissue regeneration.

overall_design:
  Digits from young (age 6 months) and aged (age 18 months) mice were harvested 10 days after amputation of the distal 1/3 of the P3 phalangeal element. For OAA treatment, aged mice were treated with OAA daily starting at day 10 post amputation and sacrificed at day 21.

citation:
  Tower RJ, Busse E, Jaramillo J, Lacey M et al. Spatial transcriptomics reveals metabolic changes underly age-dependent declines in digit regeneration. Elife 2022 May 26;11.


dataset_id: SCDS0000022
title: Single cell RNA sequencing of adult regenerating mouse digit tips
species: Mus musculus
tissues: Blastema
sex: Unknown
technologies: scRNA
disease: Digit Regeneration
submission_date: 2020-01-17 00:00:00
last_modified: 2024-07-03 00:00:00
contributors: Lehoczky JA
contacts: jlehoczky@bwh.harvard.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143888
platforms: Illumina NextSeq 500
pmid: 32097654
has_paired: STDS0000245
summary:
  Innate regeneration following digit tip amputation is one of the few examples of epimorphic regeneration in mammals. Digit tip regeneration is mediated by the blastema, the same structure invoked during limb regeneration in some lower vertebrates. By genetic lineage analyses in mice, the digit tip blastema has been defined as a population of heterogeneous, lineage restructed progenitor cells. These previous studies, however, do not comprehensively evaluate blastema heterogeneity or address lineage restruction of closely related cell types. Here we report single cell RNA sequencing of over 38,000 cells from mouse digit tip blastemas and unamputated control digit tips and generate an atlas of the cell types participating in digit tip regeneration.

overall_design:
  Adult wildtype FVB/NJ mice used to generate 5 distinct datasets throughout digit tip regeneration. The five stages are: unamputated (control), 11 days post-amputation, 12 days post-amputation, 14 days post-amputation, and 17 days post-amputation.

citation:
  Johnson GL, Masias EJ, Lehoczky JA. Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution. Dev Cell 2020 Feb 24;52(4):525-540.e5.


dataset_id: STDS0000246
species: Homo sapiens
tissues: Skin
sex: Unknown
technologies: 10x Visium
disease: Diabetic Ischemic Limb Rescue
submission_date: 2021-08-16 00:00:00
last_modified: 2022-05-05 00:00:00
contributors: Sen CK, Singh K, Rustagi Y, Srivastava R, Abouhashem AS
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182208
platforms: Illumina NovaSeq 6000
pmid: 35192691
has_paired: STDS0000246
title:
  Endothelial Phospholipase C gamma2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy

summary:
  Single-cell suspensions were generated from the unwounded human skin. Briefly, the tissue was chopped into small pieces and subjected to enzymatic dissociation using whole skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237) (Miltenyi Biotec Inc., San Diego, CA). The samples were incubated in a water bath at 37Â°C for approximately 3 hours. After incubation, the samples were diluted by adding 0.5 mL of cold cell culture medium in order to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentleMACSâ„¢ Octo dissociator and UW human skin dissociation program was performed. The cell suspension was subjected to a pre-Separation Filter, 70 Âµm, placed on a 15 mL tube in order to remove the debris. RBC were lysed using 10X RBC lysis buffer (cat. no. 420301, BioLegend, San Diego, CA). The resulting cell suspension was utilized for single cell RNA sequencing using the 10x Genomics platform using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10x Genomics, Inc.) and sequenced on an Illumina NovaSeq 6000 (Illumina, Inc).

overall_design:
  20µm thick section was taken on visium spatial gene expression slide followed by permeabilization for 12 mins. cDNA libraries were synthesized using Visium spatial gene expression reagent kit as per manufacture?s recommendations (PN-100186, 100190; 10x Genomics) and sequenced using NovaSeq 6000 (Illumina, Inc). Generated reads were pre-processed using the standard Space Ranger (https://support.10xgenomics.com/spatial-gene-expression/software) pipeline to align the raw sequencing reads onto hg38 genome and obtained the respective h5-format and spatial image files for UW human skin. Resulting pre-processed files were loaded in Seurat for further downstream data processing and analysis.

citation:
  Rustagi Y, Abouhashem AS, Verma P, Verma SS et al. Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy. Diabetes 2022 May 1;71(5):1149-1165.


dataset_id: STDS0000247
title: Spatial transcriptomics of whole mouse lung cells
species: Mus musculus
tissues: Lung
sex: Unknown
technologies: 10x Visium
disease: Normal atlas
summary: We report the distribution of mRNA in fibrotic lung sections on spatial trancriptomics sequencing.
overall_design: Examination of mouse lung samples of NS-7d, SiO2-7d, NS-7d, SiO2-56d
submission_date: 2021-09-08 00:00:00
last_modified: 2023-07-14 00:00:00
contributors: Chen M, Chao J
contacts: chaojie@seu.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183683
platforms: Illumina NovaSeq 6000
pmid: 35216634
has_paired: SCDS0000023
citation:
  Chen M, Wang J, Yuan M, Long M et al. AT2 cell-derived IgA trapped by the extracellular matrix in silica-induced pulmonary fibrosis. Int Immunopharmacol 2023 Sep;122:110545. PMID: 37390644


dataset_id: STDS0000248
title: Spatially resolved transcriptomics of high-grade serous ovarian carcinoma
species: Homo sapiens
tissues: Ovarian
sex: Unknown
technologies: 10x Visium
disease: Pan cancer
submission_date: 2021-11-29 00:00:00
last_modified: 2023-05-04 00:00:00
contributors: Stur E,Corvigno S,Xu M,Chen K,Tan Y,lee S,Liu J,Ricoo E,Krushaar D,Castro P,Zhang J,Sood A
contacts: asood@mdanderson.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189843
platforms: Illumina NovaSeq 6000
pmid: 35252817
has_paired: SCDS0000024
summary:
  Bulk and single-cell RNA sequencing do not provide full characterization of tissue spatial diversity in cancer samples, and currently available in situ techniques (multiplex immunohistochemistry, imaging mass cytometry) allow for only limited analysis of a small number of targets. The current study represents the first comprehensive approach to spatial transcriptomics of high-grade serous ovarian carcinoma using intact tumor tissue. We selected a small cohort of patients with highly annotated high-grade serous ovarian carcinoma, categorized them by response to neoadjuvant chemotherapy (poor or excellent), and analyzed pre-treatment tumor tissue specimens. Our study uncovered extensive differences in tumor composition between the poor responders and excellent responders to chemotherapy, related to cell cluster organization and localization. This in-depth characterization of high-grade serous ovarian carcinoma tumor tissue from poor and excellent responders showed that spatial interactions between cell clusters may influence chemo-responsiveness more than cluster composition alone.

overall_design:
  High-grade serous ovarian carcinoma biopsy samples from 12 female patients were collected under a protocol approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center, and all patients provided written informed consent. The fresh frozen tumor tissues were obtained from the MD Anderson Gynecologic Tumor Bank. Patients underwent a standardized therapeutic approach following chemotherapy and surgery protocols established in the Department of Gynecology Oncology & Reproductive Medicine at MD Anderson. We selected six patients with poor response to NACT with carboplatin and paclitaxel and six patients with excellent response to NACT. The definition of poor response was stable or progressive disease after three to four cycles according to radiologic evaluation and/or suboptimal interval cytoreduction after NACT according to the Response Evaluation Criteria in Solid Tumors (RECIST 1.1). Excellent responders were those with complete response or only microscopic disease left at the time of interval surgery and/or pathologic analysis after interval surgery. We did not include replicates.

citation:
  Stur E, Corvigno S, Xu M, Chen K et al. Spatially resolved transcriptomics of high-grade serous ovarian carcinoma. iScience 2022 Mar 18;25(3):103923. 


dataset_id: STDS0000249
title: Spatial transcriptomics of the mouse brain across three age groups
species: Mus musculus
tissues: Brain
sex: Unknown
technologies: 10x Visium
disease: Brain development
submission_date: 2022-09-08 00:00:00
last_modified: 2023-04-22 00:00:00
contacts: ohahn@calicolabs.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212903
platforms: Illumina NovaSeq 6000
has_paired: SCDS0000010
summary:
  Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we use the 10X Visium platform to perform spatial transcriptomics (Spatial-seq) of equivalent coronal sections of the mouse brain at young (6 months), middle (18 months) and old (21 months) age.

overall_design:
  Spatial RNA-seq of coronal brain sections from young, middle and old mice using 10x Genomics Visium for OCT embedded tissue (v3').

contributors:
  Hahn O, Foltz AG, Atkins M, Kedir B, Moran-Losada P, Munson C, Guldner I, Kern F, Pálovics R, Lu N, Lehallier B, Keller A, Wyss-Coray T


dataset_id: STDS0000250
species: Homo sapiens
tissues: Brain
sex: Unknown
technologies: 10x Visium
disease: wound repair
overall_design: spatial transcriptomics (Visium) of 14 PFA samples
submission_date: 2022-01-28 00:00:00
last_modified: 2022-10-19 00:00:00
contributors: Fu R, Norris G, Willard N, Foreman N, Donson A
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195661
platforms: Illumina NovaSeq 6000
pmid: 36215273
has_paired: SCDS0000025
title:
  Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression

summary:
  Childhood brain tumor ependymoma remains incurable in approximately 50 percent of cases. No oncogenic mechanism has been firmly established for the commonest ependymoma variant posterior fossa subgroup A (PFA), impeding clinical advances. Uncovering how heterogeneous cell types within the tumor microenvironment interact is crucial to a complete understanding of PFA disease progression. The underlying cellular components of the PFA tumor microenvironment have been revealed by single cell transcriptomics, identifying divergent epithelial differentiation and EMT lineages. Here we utilize spatial transcriptomics (Visium) of 14 PFA samples to chart neoplastic and immune cell architecture and identify novel biological processes.

citation:
  Fu R, Norris GA, Willard N, Griesinger AM et al. Spatial transcriptomic analysis delineates epithelial and mesenchymal subpopulations and transition stages in childhood ependymoma. Neuro Oncol 2023 Apr 6;25(4):786-798. PMID: 36215273


dataset_id: STDS0000251
title: Spatial transcriptomics stratifies psoriatic disease by emergent cellular ecosystems
species: Homo sapiens
tissues: Skin
sex: Unknown
technologies: 10x Visium
disease: Psoriatic disease
submission_date: 2022-05-02 00:00:00
last_modified: 2023-09-21 00:00:00
contributors: Castillo R, Sidhu I, Naik S
contacts: Shruti.Naik@nyulangone.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202011
platforms: Illumina NovaSeq 6000
pmid: 37267384
has_paired: E-MTAB-8142
summary:
  The skin is recognized as a window into the immunopathogenic mechanisms driving the vast phenotypic spectrum of psoriatic disease. To better decipher the cellular landscape of both healthy and psoriatic skin, we employed spatial transcriptomics (ST), a ground-breaking technology that precisely maps gene expression from histologically-intact tissue sections. Findings gleaned from computationally integrating our 23 matched lesional and non-lesional psoriatic and 7 healthy control samples with publicly-available single cell RNA seq data sets provided insights into the emergent cellular ecosystems at play in psoriatic disease.

overall_design:
  This is a cross-sectional study involving the accrual of 3-4-mm skin punch biopsy samples from healthy controls and biologic naïve patients with psoriatic disease. The samples were then subjected to the protocols entailed by spatial transcriptomics platform.
   	

citation:
  Castillo RL, Sidhu I, Dolgalev I, Chu T et al. Spatial transcriptomics stratifies psoriatic disease severity by emergent cellular ecosystems. Sci Immunol 2023 Jun 8;8(84):eabq7991.


dataset_id: STDS0000252
title: Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments
species: Homo sapiens
tissues: Ovarian
sex: Unknown
technologies: 10x Visium;scRNA
disease: Pan cancer
submission_date: 2022-08-24 00:00:00
last_modified: 2024-04-17 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211956
platforms: Illumina NovaSeq 6000
pmid: 38570491
has_paired: STDS0000252
summary:
  8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples obtained from the ovaries during the interval debulking surgery

overall_design:
  8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples

contributors:
  Denisenko E, de Kock L, Tan A, Beasley A, Beilin M, Jones ME, Hou R, Fox S, Hmon K, Yeow Y, Gray E, Cohen PA, Yu Y, Forrest AR, O Muiri D, Bilic S, Mohan G, Salfinger S

citation:
  Denisenko E, de Kock L, Tan A, Beasley AB et al. Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones. Nat Commun 2024 Apr 3;15(1):2860.


dataset_id: STDS0000253
species: Mus musculus
tissues: Spleen
sex: Unknown
technologies: 10x Visium
disease: T cell depletion
submission_date: 2022-04-13 00:00:00
last_modified: 2022-12-09 00:00:00
contributors: Cui W, Topchyan P
contacts: wcui04@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200720
platforms: Illumina NextSeq 500
pmid: 36450262
has_paired: SCDS0000026
title:
  Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)

summary:
  CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. Here, we applied spatial transcriptomics to explore cellular localization and potential interaction between key immune cell subsets during chronic LCMV Clone 13 infection.
   	

overall_design:
  Spleens from Control or CD4+ T cell-depleted mice on Day 7 and Day 21 post-LCMV Cl13 infection (2 mice per condition total, conducted in two separate rounds of experiments) and were frozen fresh, stored, and processed as instructed by the Visium kit (10x Genomics). 10 μm sections were generated from frozen spleens and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Spleen tissue on Visium slides was permeabilized for 18 minutes to extract mRNA and downstream library preparation and sequencing were conducted according to manufacturer’s protocol.

citation:
  Topchyan P, Zander R, Kasmani MY, Nguyen C et al. Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection. Cell Rep 2022 Nov 29;41(9):111736. PMID: 36450262


dataset_id: STDS0000254
title: Multimodal decoding of human liver regeneration [st_mouse]
species: Mus musculus
tissues: Liver
sex: Unknown
technologies: 10x Visium
disease: Liver injury regeneration
submission_date: 2023-01-24 00:00:00
last_modified: 2024-06-25 00:00:00
contributors: Matchett KP, Portman JR, Kapourani C, Wilson-Kanamori JR, Henderson NC
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223560
platforms: Illumina NovaSeq 6000
pmid: 38693268
has_paired: STDS0000128
summary:
  Using snRNA-seq combined with spatial profiling of healthy and ALF explant human livers, we uncover a novel migratory hepatocyte subpopulation. We discover a corollary subpopulation in a mouse model of APAP-induced liver regeration, and demonstrate that this subpopulation meidates wound closure following liver injury.

overall_design:
  Spatial transcriptomics was performed on mouse livers along an APAP-induced liver regeneration timecourse.

citation:
  Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA et al. Multimodal decoding of human liver regeneration. Nature 2024 Jun;630(8015):158-165. PMID: 38693268


dataset_id: STDS0000256
species: Homo sapiens
tissues: Ovarian
sex: F | M
technologies: 10x Visium
disease: Normal atlas
submission_date: 2023-03-09 00:00:00
last_modified: 2023-05-24 00:00:00
contributors: Iamshchikov P, Larionova I, Gerashchenko T, Piankov D, Koshkin P, Korostelev S, Denisov E
contacts: larionova0903irina@mail.ru
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227019
platforms: Illumina NovaSeq 6000;NextSeq 2000
pmid: 36882687
has_paired: SCDS0000024
title:
  Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

summary:
  The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics.

overall_design:
  We performed comparison of GeneMind Genolab M and Illumina NextSeq 2000 sequencing platforms using three ovarian cancer 10x Genomics Visium libraries. We evaluate performance of both platforms in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. We compared raw read mapping and read counting efficiency. Additionally, downstream analysis was performed in order to reveal concordance of dimension reduction, clusterization, and differential gene expression results between the Genolab M and NextSeq 2000 platforms. The study was carried out according to Declaration of Helsinki and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study.

citation:
  Pavel I, Irina L, Tatiana G, Denis P et al. Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics. BMC Genomics 2023 Mar 7;24(1):102. PMID: 36882687


dataset_id: STDS0000257
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: 10x Visium
disease: Pancreas development
submission_date: 2022-02-23 00:00:00
last_modified: 2022-12-24 00:00:00
contributors: Olaniru OE, Kadolsky U, Kannambath S, Vaikkinen H, Fung K, Dhami P, Persaud S
contacts: oladapo.e.olaniru@kcl.ac.uk
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197317
platforms: NextSeq 2000
pmid: 36513063
has_paired: SCDS0000027
title:
  Single cell transcriptomic and spatial landscapes of the developing human pancreas - spatial transcriptomics

summary:
  The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas.

overall_design:
  Human fetal pancreases at 12, 15, 18 and 20 post-conception weeks were subject to 10x Visium spatial transcriptomics

citation:
  Olaniru OE, Kadolsky U, Kannambath S, Vaikkinen H et al. Single-cell transcriptomic and spatial landscapes of the developing human pancreas. Cell Metab 2023 Jan 3;35(1):184-199.e5. PMID: 36513063


dataset_id: STDS0000258
title: Melanoma Brain Metastasis Atlas [SlideSeq]
species: Homo sapiens
tissues: Brain
sex: F | M
technologies: Slide-seq
disease: Melanoma metastasis
submission_date: 2022-04-06 00:00:00
last_modified: 2023-12-01 00:00:00
contributors: Izar B, Biermann J, Melms JC
contacts: jb4424@cumc.columbia.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200278
platforms: Illumina HiSeq 4000
pmid: 35803246
has_paired: SCDS0000028
summary:
  We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-seq and 17 snRNA-seq) from 21 patients and 10 treatment-naïve peripheral (extracranial) metastases (ECM; all snRNA-seq) from 10 patients. We performed matched spatial sequencing using SlideSeq2 (n=16) on 11 snRNA-seq samples.

overall_design:
  Single-cell/nuclei RNA sequencing of 22 treatment-naïve melanoma brain metastses (MBM) and 10 treatment-naïve peripheral (extracranial) metastases (ECM) with matched spatial sequencing using SlideSeqV2 (n=16) of 11 snRNA-seq samples.
  >>>Submitter states: Due to patient privacy concerns the raw data will be submitted to dbGAP.<<<

citation:
  Biermann J, Melms JC, Amin AD, Wang Y et al. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022 Jul 7;185(14):2591-2608.e30. PMID: 35803246


dataset_id: STDS0000259
species: Homo sapiens
tissues: Kidney
sex: Unknown
technologies: 10x Visium
disease: Kidney injury
submission_date: 2022-06-16 00:00:00
last_modified: 2023-08-11 00:00:00
contributors: Eadon MT, El-Achkar TM, Ferreira RM, Cheng Y
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206306
platforms: Illumina NovaSeq 6000
pmid: 37468493
has_paired: SCDS0000029
title:
  A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

summary:
  Kidney stone disease causes significant morbidity and increases health care utilization. The pathogenesis of stone disease is incompletely understood, due in part to the poor characterization of the cellular and molecular makeup of the human papilla and its alteration with disease. In this work, we characterize the human renal papilla in health and calcium oxalate stone disease using single nuclear RNA sequencing, spatial transcriptomics and high-resolution large scale multiplexed 3D and Co-Detection by indexing (CODEX) imaging. We define and localize subtypes of principal cells enriched in the papilla as well as immune and stromal cell populations. We further uncovered an undifferentiated epithelial cell signature in the papilla, particularly during nephrolithiasis.

overall_design:
  Frozen 10 µm sections were mounted on to etched frames of the Visium spatial gene expression (VSGE) slides with capture areas according to 10x Genomics protocols (Visium Spatial Protocols—Tissue Preparation Guide, Document Number CD=G000240 Rev A, 10x Genomics). H&E-stained sections were imaged with a Keyence BZ-X810 microscope equipped with a Nikon 10× CFI Plan Fluor objective at 0.7547 um/pixel and camera dimensions of 1920x1440. Stained tissues were permeabilized for 12 minutes. mRNA bound to oligonucleotides on the capture areas of the Visium slides was extracted. cDNA libraries were prepared with second strand synthesis and sequenced utilizing the NovaSeq 6000 Sequencing system (Illumina) in the 28 bp + 120 bp paired-end sequencing mode. Samples were mapped using Space Ranger 1.2.0 with the reference genome GRCh3-2020-A. The data were normalized by SCTransform and merged to build a unified UMAP and dataset.

citation:
  Canela VH, Bowen WS, Ferreira RM, Syed F et al. A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. Nat Commun 2023 Jul 19;14(1):4140. PMID: 37468493


dataset_id: STDS0000260
title: Bacterial TLR2/6 Ligands Block Ciliogenesis, Derepress Hedgehog Signaling, and Expand the Neocortex
species: Mus musculus
tissues: Brain
sex: Unknown
technologies: 10x Visium
disease: Bacterial
submission_date: 2023-04-13 00:00:00
last_modified: 2023-04-16 00:00:00
contributors: Crawford JC, Mann B, Tuomanen EI
contacts: jeremy.crawford@stjude.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE229699
platforms: Illumina NovaSeq 6000
pmid: 37052506
has_paired: SCDS0000010
summary:
  Microbial components have a range of direct effects on the fetal brain. However, little is known about the cellular targets and molecular mechanisms that mediate these effects. Neural progenitor cells (NPCs) control the size and architecture of the brain and understanding the mechanisms regulating NPCs is crucial to understanding brain developmental disorders. We identify ventricular radial glia (vRG), the primary NPC, as the target of bacterial cell wall (BCW) generated during the antibiotic treatment of maternal pneumonia. BCW enhanced proliferative potential of vRGs by shortening the cell cycle and increasing self-renewal. Expanded vRGs propagated to increase neuronal output in all cortical layers. Remarkably, Toll-like receptor 2 (TLR2), which recognizes BCW, localized at the base of primary cilia in vRGs and the BCW-TLR2 interaction suppressed ciliogenesis leading to derepression of Hedgehog (HH) signaling and expansion of vRGs. We also show that TLR6 is an essential partner of TLR2 in this process. Surprisingly, TLR6 alone was required to set the number of cortical neurons under healthy conditions. These findings suggest that an endogenous signal from TLRs suppresses cortical expansion during normal development of the neocortex and that BCW antagonizes that signal through the TLR2/cilia/HH signaling axis changing brain structure and function.

overall_design:
  Comparative spatial transcriptomics of mouse brain sections obtained at E12 after either S. pneumoniae + ampicillin challenge or after ampicillin control.

citation:
  Mann B, Crawford JC, Reddy K, Lott J et al. Bacterial TLR2/6 Ligands Block Ciliogenesis, Derepress Hedgehog Signaling, and Expand the Neocortex. mBio 2023 Jun 27;14(3):e0051023. PMID: 37052506


dataset_id: STDS0000261
title: Visium Analysis of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution
species: Homo sapiens
tissues: Head Neck
sex: Unknown
technologies: 10x Visium
disease: Head and neck squamous carcinoma (HNSCC)
overall_design: 10X Visium Spatial transcriptome Sequencing of HNSCC pateint tumor in different part
submission_date: 2021-08-02 00:00:00
last_modified: 2022-08-30 00:00:00
contributors: Yang M, Tai S, Chung C
contacts: senisc@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181300
platforms: Illumina NovaSeq 6000
pmid: 36002186
has_paired: SCDS0000030
summary:
  We collected HNSCC primary tumor sections from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for 10x Genomics Visium analysis.

citation:
  Cheng HY, Hsieh CH, Lin PH, Chen YT et al. Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance. J Immunother Cancer 2022 Aug;10(8). PMID: 36002186


dataset_id: STDS0000262
title: Pharmacological targeting Netrin-1 inhibits EMT in cancer [Visium]
species: Mus musculus
tissues: Skin
sex: Unknown
technologies: 10x Visium
disease: Cancer
submission_date: 2023-06-06 00:00:00
last_modified: 2023-08-16 00:00:00
contributors: Lengrand J, Vanuytven S, Song Y, Blanpain C
contacts: sebastiaan.vanuytven@ulb.be
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234266
platforms: Illumina NovaSeq 6000
pmid: 37532929
has_paired: SCDS0000031
summary:
  Epithelial-to-Mesenchymal transition (EMT) regulates tumour initiation, progression, metastasis and resistance to anti-cancer therapy. Whereas great progress had recently been made in understanding the role and mechanisms that regulate EMT in cancer, no therapeutic strategy to pharmacologically target EMT had been identified so far. Here, we found that Netrin-1 is upregulated in a primary mouse model of skin squamous cell carcinoma (SCCs) presenting spontaneous EMT. Pharmacological inhibition of Netrin-1 by administrating NP137, an anti-Netrin-1 blocking monoclonal antibody currently used in clinical trials in human cancer, decreased the proportion EMT tumour cells in skin SCCs, as well as decreased the number of metastasis and increased the sensitivity of tumour cells to chemotherapy. Single-cell RNA-seq revealed the presence of different EMT states including epithelial, early and late hybrid EMT as well as fully EMT states in control SCCs. In contrast, administration of NP137 prevents the progression of cancer cells towards a late EMT state and sustains tumour epithelial states. ShRNA knockdown (KD) of Netrin-1 and its receptor Unc5b in EPCAM+ tumour cells inhibited EMT in vitro in the absence of stromal cells and regulated a common gene signature promoting tumour epithelial state and restricting EMT. To assess the relevance of these findings to human cancers, we treated mice transplanted with A549 human cancer cell line that undergoes EMT following TGF-b1 administration with NP137. Netrin-1 inhibition decreased EMT in A549 cells in vivo. Altogether, our results identify a new pharmacological strategy to target EMT in cancer opening novel therapeutic interventions for anti-cancer therapy.

overall_design:
  To induce tumorigenesis on Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ (LKPR), Tamoxifen was diluted at 25 mg/ml in sunflower seed oil, 10% EtOH (Sigma). Four daily intraperitoneal (IP) injections of 2.5 mg tamoxifen were administered at P28 to LKPR mice. After 7-9 week after Tamoxifen injection tumour appearance and size were detected by daily observation and palpation. Mice were euthanized when tumour size was reached or when mice presented signs of distress. To determine the effect of anti-Netrin-1 molecule (NP137) on primary tumour, LKPR mice were treated intraperitoneally at 10 mg/kg every two days from 4 weeks after Tamoxifen injection and until the death of animal. Control and NP137-treated skin tumours from LKPR mice were dissected, rinsed one part of the tumors has been kept for immunochemistry. Tumour tissues were pre-fixed in 4% PFA for 2 h at room temperature, rinsed in PBS, before to be embedded in FFPE. To analyze the spatial distribution and localization of different EMT tumors states previously described by scRNA-seq in Control and anti-Netrin-1 treated skin SCC tumors, we used VISIUM technology for spatial transcriptomic analysis (10X Genomics). FFPE tissue section were places on Visium slides and prepared according to 10X Genomics protocols. After H&E staining, imaging and decrosslinking steps, tissue sections were incubated with human specific probes targeting 10,551 genes (10X genomics, Visium Mouse Transcriptome probe Set v1.0).

citation:
  Lengrand J, Pastushenko I, Vanuytven S, Song Y et al. Pharmacological targeting of netrin-1 inhibits EMT in cancer. Nature 2023 Aug;620(7973):402-408. PMID: 37532929


dataset_id: STDS0000263
title: mousemodel_Heptablastoma spatial transcriptomics
species: Mus musculus
tissues: Blastema
sex: Unknown
technologies: 10x Visium
disease: ‌Heptablastoma cancer
submission_date: 2022-01-27 00:00:00
last_modified: 2023-09-08 00:00:00
contributors: Fang J, Singh S, Natarajan S, Yang J, Chen X
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195575
platforms: Illumina NovaSeq 6000
pmid: 37414763
has_paired: SCDS0000032
summary:
  Lack of relevant animal models and cell lines hampers the understanding of hepatoblastoma and identification of therapeutic targets. We report a hepatoblastoma murine model that faithfully recapitulates the pathological features of mixed fetal and embryonic hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of human disease

overall_design:
  Flash Frozen Tumor was harvested from Hepatocellular model. Spatial Tx data was generated using Visium Spatial Gene expression kit from 10X genomics. The H&E images were acuqired using Zeiss- AxioScan slide scanner.

citation:
  Fang J, Singh S, Cheng C, Natarajan S et al. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun 2023 Jul 6;14(1):4003.


dataset_id: STDS0000264
title: Visium Spatial Transcriptomics of a murine model of IPMN
species: Mus musculus
tissues: Pancreas
sex: Unknown
technologies: 10x Visium
disease: Pancreatic cancer
submission_date: 2023-05-24 00:00:00
last_modified: 2023-09-06 00:00:00
contributors: Sans M, Rajapakshe KI, Makino Y, Min J, Guerrero PA, Maitra A
contacts: AMaitra@mdanderson.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233317
platforms: NextSeq 550
pmid: 37285225
has_paired: SCDS0000033
summary:
  Pancreata were collected from two Kras;Gnas mice and analyzed by Visium Spatial Gene Expression to evaluate the transcriptional profile associated with NKX6-2 that was observed in the human IPMN samples.

overall_design:
  Samples were collected from mice at 15 and 25 weeks post doxycycline treatment and were flash frozen. The samples were then cryosectioned and analyzed with the Visium Spatial Gene Expression platform from 10x genomics.

citation:
  Sans M, Makino Y, Min J, Rajapakshe KI et al. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential. Cancer Discov 2023 Aug 4;13(8):1844-1861. PMID: 37285225


dataset_id: STDS0000265
title: Visium Spatial Transcriptomics expression profiles from IPMN samples of the pancreas
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: 10x Visium
disease: Pancreatic cancer
submission_date: 2023-05-24 00:00:00
last_modified: 2023-09-06 00:00:00
contributors: Sans M, Rajapakshe KI, Guerrero PA, Maitra A
contacts: AMaitra@mdanderson.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233293
platforms: Illumina NextSeq 500
pmid: 37285225
has_paired: SCDS0000034
summary:
  Intraductal Papillary Mucinous Neoplasms (IPMN) are pancreatic mucinous cysts that can progress to cancer. We used spatial transcriptomics to characterize the epithelium and microenvironment of IPMN samples of different grades and histological subtypes.

overall_design:
  Spatial transcriptomic experiments were conducted on fresh frozen IPMN specimens with the Visium Spatial Gene Expression platform from 10x genomics.

citation:
  Sans M, Makino Y, Min J, Rajapakshe KI et al. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential. Cancer Discov 2023 Aug 4;13(8):1844-1861. PMID: 37285225


dataset_id: STDS0000266
species: Mus musculus
tissues: Embryo
sex: Unknown
technologies: 10x Visium
disease: Zika virus
submission_date: 2022-06-07 00:00:00
last_modified: 2023-09-03 00:00:00
contributors: Aagaard K, Barrozo E, Jochum M
contacts: michael.jochum@bcm.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205631
platforms: Illumina NovaSeq 6000
pmid: 37598997
has_paired: SCDS0000035
title:
  Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [visium]

summary:
  We and others have demonstrated Zika virus (ZIKV) congenital infection evades double-stranded RNA detection, and may persist in the placenta for the duration of pregnancy without accompanying overt histopathologic inflammation. We used orthogonal approaches to test the hypothesis that ZIKV disrupts placental miRNAs to enable viral persistence and fetal pathogenesis. In primary human trophoblasts, high-throughput sequencing crosslinking and immunoprecipitation (AGO-HITS-CLIP) demonstrated an unexpected disruption of placental miRNA-regulated TGF-β networks. In gnotobiotic mice, absence of microbes rendered normally resistant mice susceptible to congenital ZIKV infection, and placental spatial transcriptomics revealed distinct microenvironments defined by significant upregulation of complement cascade components. Finally, treatment of ZIKV-infected mice with the RNAi-enhancer enoxacin led to loss of ZIKV placental persistence and rescue of fetal growth restriction. These results collectively suggest that ZIKV co-opts miRNA inflammatory regulatory networks to persist in the placenta reservoir, a conduit of vertical transmission and fetal pathogenesis.
   	

overall_design:
  Gnotobiotic congenital ZIKV mouse model. Following timed mattings of four-to-six-week-old Swiss/webster mice from the Baylor College of Medicine Gnotobiotics Core, plugged dams were weighed and transferred to separate sterile insulators. Daily intraperitoneal injections of enoxacin (Sigma-Aldrich, Cat. 557304) at 10 mg/kg were previously shown to be safe and effective in a model of obesity32 and were done from embryonic days E1.5-E18.5. Dams were either received mock United States Pharmacopeia (USP)-grade phosphate-buffered saline (PBS) (VWR, Cat. 76081-514) subdermal injections or ZIKV infection with HN16 strain (first passage in Vero-E6 cells) at an MOI of 1x105 PFU on embryonic days E7.5, E8.5, and E9.5. On day 18.5, dams were humanely sacrificed, and uterine horns were dissected. Images of the uterine horns were taken to record resorption events. Individual fetuses were weighed. Placental tissues were stored at -80C in Trizol. All mouse experiments were conducted under the supervision of Baylor College of Medicine Institutional Animal Care and Use Committee approved protocols.

citation:
  Barrozo ER, Seferovic MD, Hamilton MP, Moorshead DN et al. Zika virus co-opts microRNA networks to persist in placental niches detected by spatial transcriptomics. Am J Obstet Gynecol 2024 Feb;230(2):251.e1-251.e17. PMID: 37598997


dataset_id: STDS0000267
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: 10x Visium
disease: Pancreatic cancer
overall_design: spatial transcriptome was performed in 4 PDAC patient tumor samples with neuropathy.
submission_date: 2022-05-11 00:00:00
last_modified: 2023-05-31 00:00:00
contacts: xuemeilin@sjtu.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202740
platforms: Illumina NovaSeq 6000
has_paired: SCDS0000036
title:
  Schwann Cells Shape Tumor Cells and Cancer-Associated Fibroblasts in the Pancreatic Ductal Adenocarcinoma Microenvironment [ST]

summary:
  Neuropathy is a feature more frequently observed in pancreatic ductal adenocarcinoma (PDAC) than other tumors. Schwann cells, the most prevalent cell in peripheral nerves, migrate toward tumor cells and associate with poor prognosis in PDAC. To unveil the effects of Schwann cells on the neuro-stroma niche, single-cell RNA-sequencing and microarray-based spatial transcriptome analysis of PDAC tissues were performed. Results suggested that Schwann cells may drive tumor cells and cancer-associated fibroblasts (CAFs) to more malignant subtypes: basal-like and inflammatory CAFs (iCAFs), respectively. Moreover, in vitro and in vivo assays demonstrated that Schwann cells enhanced the proliferation and migration of PDAC cells via Midkine and promoted the switch of CAFs to iCAFs via interleukin-1a. By Schwann cells condition medium, tumor cells together with iCAFs accelerate PDAC progression. Thus, we revealed, for the first time, that Schwann cells induce malignant subtypes of tumor cells and CAFs in the PDAC milieu.

contributors:
  Xue M, Zhu Y, Jiang Y, Han L, Shi M, Su R, Wang L, Xiong C, Wang C, Wang T, Wu D, Cao Y, Dong L, Bai F, Zhao S, Deng X, Peng C, Li H, Chen J, Shen B, Jiang L, Chen H


dataset_id: STDS0000268
species: Mus musculus
tissues: Heart
sex: Unknown
technologies: 10x Visium
disease: Neonatal heart regeneration
submission_date: 2022-06-29 00:00:00
last_modified: 2024-02-20 00:00:00
contributors: Cui M, Olson E
contacts: miaocui713@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207215
platforms: Illumina NextSeq 500
has_paired: SCDS0000037
title:
  The PD-1/PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration [Spatial]

summary:
  The adult heart responds to injury by scarring with consequent loss of contractile function, whereas the neonatal heart possesses the ability to regenerate. We compared the immune response to injury in neonatal and adult mouse hearts and discovered that the PD1/PD-L1 immune checkpoint pathway is highly activated in regenerative hearts but is silenced in later life. Deletion of the PD1 receptor or inactivation of its PD-L1 ligand prevented regeneration of neonatal hearts after injury. Our findings reveal a previously unrecognized role of the PD1/PD-L1 pathway in the control of heart regeneration through modulating T cell activity and inflammation following injury and provide new inroads into the control of adult tissue regeneration.

overall_design:
  We analyzed spatial transcriptome transverse sections collected from PD1 homozygous and heterozygous heart at 7 days after myocardial infarction performed at P2.


dataset_id: STDS0000269
title: Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section
species: Homo sapiens;Mus musculus
tissues: Brain
sex: Unknown
technologies: 10x Visium
disease: Normal atlas
submission_date: 2023-05-19 00:00:00
last_modified: 2023-05-23 00:00:00
contacts: marcovicari3@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232910
platforms: NextSeq 2000
has_paired: SCDS0000010
summary:
  We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.

overall_design:
  Tissue sections processed with MALDI-MSI were eventually analyzed using Visium. Controls for some of the samples are included.
  *** From Submitter: We are restricted to deposit raw sequencing from humans to SRA. Those will be deposited on the Swedish federated EGA node and we will link when it became available to us. ***

contributors:
  Vicari M, Mirzazadeh R, Nilsson A, Shariatgorji R, Bjärterot P, Larsson L, Lee H, Nilsson M, Foyer J, Ekvall M, Czarnewski P, Zhang X, Svenningsson P, Andrén PE, Lundeberg J


dataset_id: STDS0000270
species: Homo sapiens
tissues: Skin
sex: Unknown
technologies: 10x Visium
disease: Psoriasis
overall_design: Visium spatial sequencing comparing psoriasis skin to healthy control skin samples
submission_date: 2023-02-16 00:00:00
last_modified: 2023-08-07 00:00:00
contributors: Ma F, Plazyo O, Gudjonsson JE
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225475
platforms: Illumina NovaSeq 6000
pmid: 37308489
has_paired: E-MTAB-8142
title:
  Single Cell and Spatial Sequencing Define Processes by which Keratinocytes and Fibroblasts Amplify Inflammatory Responses in Psoriasis

summary:
  The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is incompletely understood. Here we demonstrate, using a combination of single cell and spatial RNA sequencing, IL-36 dependent amplification of IL-17A and TNF inflammatory responses in the absence of neutrophil proteases, which primarily occurred within the supraspinous layer of the psoriatic epidermis. We further show that a subset of SFRP2+ fibroblasts in psoriasis contribute to amplification of the immune network through transition to a pro-inflammatory state. The SFRP2+ fibroblast communication network involves production of CCL13, CCL19 and CXCL12, connected by ligand-receptor interactions to other spatially proximate cell types: CCR2+ myeloid cells, CCR7+ LAMP3+ dendritic cells, and CXCR4 expressed on both CD8+ Tc17 cells and keratinocytes, respectively. The SFRP2+ fibroblasts also express cathepsin S, further amplifying inflammatory responses by activating IL-36G in keratinocytes. These data provide an unprecedented view of psoriasis pathogenesis, which expands our understanding of the critical cellular participants to include inflammatory fibroblasts and their cellular interactions.

citation:
  Ma F, Plazyo O, Billi AC, Tsoi LC et al. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat Commun 2023 Jun 12;14(1):3455. PMID: 37308489


dataset_id: SCDS0000023
title: Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing
species: Mus musculus
tissues: Lung
sex: Unknown
technologies: scRNA
disease: Lung fibrosis
submission_date: 2019-04-10 00:00:00
last_modified: 2019-04-14 00:00:00
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129605
platforms: Illumina NextSeq 500
pmid: 30848683
has_paired: STDS0000247
summary:
  In brief, we have applied a novel and unbiased approach to identify distinct and dynamic cell populations, including an in-depth analysis of the fibroblast population, in lung fibrosis. We found that while fibroblast number did not increase after injury, a population of activated fibroblasts can be identified in the fibrotic mouse lung. Using expression profiles of 1,945 lung fibroblasts we redefine the molecular characteristics of activated fibroblasts, finding that they are not a separate population but rather exhibit a similar, yet amplified, gene expression pattern to non-activated cells.

overall_design:
  A bolus of Bleomycin (2.8 U/kilogram (kg); 1.75 milligram (mg)/kg) or 0.9% sterile saline at 2ml/kg volume was dosed into mouth of each C57BL/6 male mouse (12-13 weeks) near the larynx to induce lung fibrosis. 3 Groups: Saline Control, Bleomycin, and Bleomycin+60mg/kg Nintedanib treatment was started concomitantly with the administration of bleomycin and single cell isolations were performed on day 11.

contributors:
  Peyser R, MacDonnell S, Gao Y, Cheng L, Kim Y, Kaplan T, Ruan Q, Wei Y, Ni M, Adler C, Zhang W, Devalaraja-Narashimha K, Grindley J, Halasz G, Morton L

citation:
  Peyser R, MacDonnell S, Gao Y, Cheng L et al. Defining the Activated Fibroblast Population in Lung Fibrosis Using Single-Cell Sequencing. Am J Respir Cell Mol Biol 2019 Jul;61(1):74-85


dataset_id: SCDS0000024
species: Homo sapiens
tissues: Ovarian
sex: Unknown
technologies: scRNA
disease: Gynecological cancer
overall_design: landscape of HGSOC ecosystem
submission_date: 2021-09-27 00:00:00
last_modified: 2022-06-11 00:00:00
contributors: Xu J
contacts: xjfzu@zju.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184880
platforms: Illumina NovaSeq 6000
pmid: 35675036
has_paired: STDS0000248
title:
  Single-cell RNA sequencing reveals tissue architecture during human high-grade serous ovarian cancer progression

summary:
  As the most fatal type of gynecological cancers, high-grade serous ovarian cancer (HGSOC) exhibits heterogeneity that obstacles therapeutics. Up to date, the pathogenesis of HGSOC remains poorly understood. Here, we performed the deep single-cell RNA sequencing (scRNA-seq) using 59,324 cells isolated from seven treatment-naïve HGSOC patients at early or late tumor stages and five age-matched non-malignant ovarian samples. Our sequencing data showed a highly complex ecosystem of tumor, immune and stromal cells based on their marker genes and functional properties. We showed that normal ovary-specific fibroblasts were carried with the properties of mesenchymal stem cells (MSCs), which could be reprogrammed to cancer-associated fibroblasts. During tumor progression, matrix CAFs (mCAFs) could induce the EMT properties of the tumor cells. Furthermore, the analysis of the early stage tumors illuminated enrichments of IDO-expressing macrophages, CD8+ TRM cells, and the activated CD8+ TEX cells (TRM-CXCL13), whereas those tumors at the late stages loss these features and expressed signatures related to epithelial-to-mesenchymal transition (EMT) program. Also, we characterized a specific chemokine-receptor communication in HGSOC tumor microenvironment, which may contribute to shape the HGSOC features. Our compendia of scRNA-seq results provide valuable insights for understanding the landscape of HGSOC ecosystem, which will be helpful in advancing HGSOC cancer diagnosis and therapy and enabling personalized approaches to the treatment.

citation:
  Xu J, Fang Y, Chen K, Li S et al. Single-Cell RNA Sequencing Reveals the Tissue Architecture in Human High-Grade Serous Ovarian Cancer. Clin Cancer Res 2022 Aug 15;28(16):3590-3602.


dataset_id: SCDS0000025
title: Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas (scRNA-Seq)
species: Homo sapiens
tissues: Brain
sex: Unknown
technologies: scRNA
disease: Pediatric gliomas
overall_design: 37 patient tumors analysed by scRNA-seq.
submission_date: 2022-08-04 00:00:00
last_modified: 2022-08-07 00:00:00
contacts: claudia.kleinman@mcgill.ca
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210567
platforms: Illumina HiSeq 4000
has_paired: STDS0000250
summary:
  Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations, and molecular profiles. The contribution of the cell-of-origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte-precursor-like cells (OPC). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, while H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, while other epigenetic changes are mainly contingent on the cell-of-origin chromatin state and cycling rate.

contributors:
  Jessa S,Mohammadnia A,Harutyunyan AS,Hulswit M,Varadharajan S,Lakkis H,Kabir N,Bashardanesh Z,HÃ©bert S,Faury D,Vladoiu MC,Worme S,Coutelier M,Krug B,Andrade AF,Pathania M,Bajic A,Weil AG,Ellezam B,Atkinson J,Dudley RR,Farmer J,Perreault S,Garcia BA,Larouche V,Blanchette M,Garzia L,Bhaduri A,Ligon KL,Bandopadhayay P,Taylor MD,Mack SC,Jabado N,Kleinman CL


dataset_id: SCDS0000026
species: Mus musculus
tissues: Ovarian
sex: Unknown
technologies: scRNA
disease: Normal atlas
summary: We have created a resource of single cell transcriptome data from the model organism Mus musculus.
overall_design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
submission_date: 2018-01-29 00:00:00
last_modified: 2019-06-04 00:00:00
contributors: Angela Oliveira Pisco
contacts: angela.pisco@czbiohub.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109774
platforms: Illumina NovaSeq 6000
pmid: 30283141
has_paired: STDS0000253
title:
  Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution

citation:
  Tabula Muris Consortium, Overall coordination, Logistical coordination, Organ collection and processing et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 2018 Oct;562(7727):367-372.


dataset_id: SCDS0000027
title: Single cell transcriptomic and spatial landscapes of the developing human pancreas
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: scRNA;10x Visium
disease: Pancreas development
submission_date: 2022-02-20 00:00:00
last_modified: 2022-12-24 00:00:00
contributors: Olaniru OE,Kadolsky U,Kannambath S,Vaikkinen H,Fung K,Dhami P,Persaud S
contacts: oladapo.e.olaniru@kcl.ac.uk
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197064
platforms: Illumina HiSeq 2500
pmid: 36513063
has_paired: STDS0000257
summary:
  The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas.

overall_design:
  Human fetal pancreases at 12, 13, 14, 15, 18, 19 and 20 post-conception weeks were subject to single cell RNA-seq analysis

citation:
  Olaniru OE, Kadolsky U, Kannambath S, Vaikkinen H et al. Single-cell transcriptomic and spatial landscapes of the developing human pancreas. Cell Metab 2023 Jan 3;35(1):184-199.e5.


dataset_id: SCDS0000028
title: Single cell RNA-seq of brain glioblastoma samples
species: Homo sapiens
tissues: Brain
sex: Unknown
technologies: scRNA
disease: Glioblastomas
submission_date: 2020-12-03 00:00:00
last_modified: 2021-07-08 00:00:00
contributors: Zhang L,Yuan X,Dimberg A,Wang L,Betsholtz C
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162631
platforms: Illumina NovaSeq 6000
pmid: 34228647
has_paired: STDS0000258
summary:
  Glioblastomas (GBM) are the most aggressive type of brain tumors with a dismal prognosis. The effectiveness of anti-tumor drugs is thwarted by brain endothelial cells (ECs) in the tumor microenvironment. However, the characteristics of ECs remains poorly inventoried at the single-cell level. We performed single-cell RNA sequencing (scRNA-seq) for ECs from 4 GBMs and matching non-malignant brain samples, and identified distinct EC phenotypes in GBM.

overall_design:
  We profiled freshly isolated cells from tumor core and paired surrounding peripheral tissue in 4 glioblastoma patients. Single-cell suspensions, magnetic-activated cell sorting (MACS) enriched for CD31+ cells, were subjected to scRNA-seq using a 10X genomics-based single-cell protocol.

citation:
  Xie Y, He L, Lugano R, Zhang Y et al. Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing. JCI Insight 2021 Aug 9;6(15).


dataset_id: SCDS0000029
title: Construction of A Human Cell Landscape by Single-cell mRNA-seq
species: Homo sapiens
tissues: Kidney
sex: Unknown
technologies: scRNA
disease: Normal atlas
submission_date: 2019-07-16 00:00:00
last_modified: 2022-08-02 00:00:00
contributors: Guo G,Han X,Zhou Z,Fei L,Sun H,Wang R,Wang J,Chen H
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134355
platforms: HiSeq X Ten
pmid: 32214235
has_paired: STDS0000259
summary:
  We used single-cell RNA sequencing to determine the cell type composition of all major human organs and construct a basic scheme for the human cell landscape (HCL). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously. We present a âsingle-cell HCL analysisââ pipeline that accurately defines human cell types and exemplify its utility in stem cell biology. Finally, we perform single-cell comparative analysis of the human and mouse cell atlases to reveal the conserved genetic networks in the mammalian system.

overall_design:
  Microwell-seq analyses of 60 types of human tissues and supplementary datasets  for the Mouse Cell Atlas data.

citation:
  Han X, Zhou Z, Fei L, Sun H et al. Construction of a human cell landscape at single-cell level. Nature 2020 May;581(7808):303-309.


dataset_id: SCDS0000030
title: Investigation of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution
species: Homo sapiens
tissues: Head Neck
sex: Unknown
technologies: scRNA
disease: Squamous carcinoma
overall_design: RNA Sequencing of HNSCC pateint tumor in different part
submission_date: 2021-06-21 00:00:00
last_modified: 2023-09-14 00:00:00
contributors: Yang M,Tai S,Chung C
contacts: senisc@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178537
platforms: Illumina HiSeq 2500
pmid: 36002186
has_paired: STDS0000261
summary:
  We collected matched pairs of primary tumor (invasive front and intra-tumor region), metastatic region and adjacent normal tissue from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for RNA sequencing analysis.

citation:
  Cheng HY, Hsieh CH, Lin PH, Chen YT et al. Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance. J Immunother Cancer 2022 Aug;10(8).


dataset_id: SCDS0000032
title: Mouse model of Heptablastoma
species: Mus musculus
tissues: Blastema
sex: Unknown
technologies: scRNA
disease: hepatoblastoma murine
submission_date: 2022-01-20 00:00:00
last_modified: 2023-09-08 00:00:00
contributors: Fang J,Singh S,Natarajan S,Yang J,Chen X
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194051
platforms: Illumina NovaSeq 6000
pmid: 37414763
has_paired: STDS0000263
summary:
  Lack of relevant animal models and cell lines hampers the understanding of hepatoblastoma and identification of therapeutic targets. We report a  hepatoblastoma murine model that faithfully recapitulates the pathological features of mixed fetal and embryonic hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of human disease

overall_design:
  Tumor was analyzed from Hepatocellular model at single cell RNA sequencing. The ScRNAseq was performed using 10X genomics -Single cell gene expression kit.

citation:
  Fang J, Singh S, Cheng C, Natarajan S et al. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun 2023 Jul 6;14(1):4003.


dataset_id: SCDS0000033
title: The role of Fgf9 in mouse pancreas development [scRNA-seq]
species: Mus musculus
tissues: Pancreas
sex: Unknown
technologies: scRNA
disease: Pancreas development
submission_date: 2022-08-05 00:00:00
last_modified: 2023-05-12 00:00:00
contributors: Sneddon J,Patzek S,Liu Z,de la O S
contacts: Julie.Sneddon@ucsf.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210645
platforms: Illumina NovaSeq 6000
pmid: 37096042
has_paired: STDS0000264
summary:
  Temporally and spatially coordinated epithelialâmesenchymal interactions are central to the development of the primitive gut tube endoderm and are necessary to form functional organs of the gastrointestinal tract, including the pancreas. Here, we examined the functional role of the secreted factor Fgf9 in murine pancreatic development. Single-cell RNA-sequencing was performed on embryonic day (E) 14.5 mouse pancreas from both wildtype and Fgf9 knockout embryos. Our data reveal shifts in cellular populations upon loss of Fgf9. In addition, we have identified specific transcriptional programs and signaling pathways perturbed in the context of loss of Fgf9 during pancreatic development.

overall_design:
  We profiled embryonic pancreas from Fgf9-LacZ mice (3 pancreata from 3 litters pooled into a single Null sample), in which a LacZ cassette has been inserted into the Fgf9 locus, rendering it a functional knockout. Fgf9 replete littermates (8 pancreata from 3 litters pooled into a single Control sample) served as corresponding control.

citation:
  Patzek S, Liu Z, de la O S, Chang S et al. Loss of Fgf9 in mice leads to pancreatic hypoplasia and asplenia. iScience 2023 Apr 21;26(4):106500. 


dataset_id: SCDS0000034
title: Visium Spatial Transcriptomics expression profiles from IPMN samples of the pancreas
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: scRNA
disease: Intraductal Papillary Mucinous Neoplasms cancer
submission_date: 2023-05-24 00:00:00
last_modified: 2023-09-06 00:00:00
contributors: Sans M,Rajapakshe KI,Guerrero PA,Maitra A
contacts: AMaitra@mdanderson.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233293
platforms: Illumina NextSeq 500
pmid: 37285225
has_paired: STDS0000265
summary:
  Intraductal Papillary Mucinous Neoplasms (IPMN)  are pancreatic mucinous cysts that can progress to cancer. We used spatial transcriptomics to characterize the epithelium and microenvironment of IPMN samples of different grades and histological subtypes.

overall_design:
  Spatial transcriptomic experiments were conducted on fresh frozen IPMN specimens with the Visium Spatial Gene Expression platform from 10x genomics.

citation:
  Sans M, Makino Y, Min J, Rajapakshe KI et al. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential. Cancer Discov 2023 Aug 4;13(8):1844-1861.


dataset_id: SCDS0000035
species: Mus musculus
tissues: Embryo
sex: Unknown
technologies: scRNA
disease: Gestation development
submission_date: 2021-06-15 00:00:00
last_modified: 2022-05-25 00:00:00
contributors: Tosevska A,Ghosh S,Devaskar S,Pellegrini M
contacts: sghoshucla@ucla.edu, pshubhamoy@gmail.com
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178229
platforms: Illumina NovaSeq 6000
pmid: 35589747
has_paired: STDS0000266
title:
  Examination of cell type specific gene expression pattern in placenta of mouse exposed to Air-pollutant material during gestation.

summary:
  We  are reporting  the expression pattern of placental transcriptome in a celltype specific manner from Gestational D19 mouse exposed to Air -Pollutant material.

overall_design:
  Placenta was collected from gestational Day19 (D19) of C57BL/6J mouse either exposed to air pollutant material or sterile PBS during the entire gestation period (from D1 of conception to D18). Three different compartments of placenta (Decidua, Junction and Labyrinth) were separated under the microscope and single cell suspension was prepared to make scRNA sequencing library.

citation:
  Tosevska A, Ghosh S, Ganguly A, Cappelletti M et al. Integrated analysis of an in vivo model of intra-nasal exposure to instilled air pollutants reveals cell-type specific responses in the placenta. Sci Rep 2022 May 19;12(1):8438. 


dataset_id: SCDS0000036
title: Single-cell RNA-seq reveals immune landscape of pancreatic cancer
species: Homo sapiens
tissues: Pancreas
sex: Unknown
technologies: scRNA
disease: Pancreatic cancer
submission_date: 2022-09-08 00:00:00
last_modified: 2023-08-10 00:00:00
contributors: Chen K
contacts: Drchenkai@pku.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212966
platforms: Illumina NovaSeq 6000
pmid: 36944944
has_paired: STDS0000267
summary:
  Pancreatic ductal adenocarcinoma (PDAC) has complex tumor immune microenvironment (TIME), the clinical values of which remains to be explored. This study aimed to delineate the immune landscape of PDAC and determine the clinical value of immune features in TIME. There was a significant difference in immune profiles between PDAC and adjacent normal pancreatic tissues. Several novel immune features were captured by quantitative pathology analysis on mIHC, some of which were significantly correlated to the prognosis of PDAC patients. A risk score-based prognostic model was developed according to these immune features. We also drew a user-friendly nomogram plot to predict the overall survival of patients by combining risk score and clinicopathologic features. Both mIHC and scRNA-seq analyses showed the expression of PD-L1 was scarce in PDAC. We found that PD1+ cells were distributed in different T cell subpopulations, not enriched in a specific subpopulation. In addition, there were other conserved receptor-ligand pairs (CCL5-SDC1/4) besides PD1-PD-L1 interaction between PD1+ T cells and PD-L1+ tumor cells. Our findings reveal the immune landscape of PDAC and highlight the significant value of combined application of mIHC and scRNA-seq in uncovering TIME, which might provide new clues for developing immunotherapy strategies.

overall_design:
  All H&E stained slides from eighty patients were reviewed for confirming PDAC diagnosis by a pathologist. The corresponding tumor and adjacent noncancerous areas were carefully marked. Duplicated 1.5 mm diameter tissue cores were selectively punched and transferred to recipient tissue array blocks. The tissue microarray (TMA) was set up. For scRNA-seq analysis, a total of six PDAC and six adjacent noncancerous resection specimens were obtained from the Department of General Surgery at Peking University First Hospital. All patients with PDAC did not receive any treatments before collecting specimens.

citation:
  Chen K, Wang Q, Liu X, Tian X et al. Immune profiling and prognostic model of pancreatic cancer using quantitative pathology and single-cell RNA sequencing. J Transl Med 2023 Mar 21;21(1):210.


dataset_id: SCDS0000037
species: Mus musculus
tissues: Heart
sex: Unknown
technologies: scRNA
disease: Heart failure
submission_date: 2021-07-03 00:00:00
last_modified: 2021-12-21 00:00:00
contributors: Wu T,Liang Z,Chen J
contacts: juchen@health.ucsd.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179390
platforms: Illumina NovaSeq 6000
pmid: 34915728
has_paired: STDS0000268
title:
  PRDM16 Functions as A Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle (scRNA-seq)

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 E13.5 WT heart samples and two E13.5 Prdm16cKO heart samples (each sample included 3-4 individual hearts) were used for scRNA-seq.

citation:
  Wu T, Liang Z, Zhang Z, Liu C et al. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle. Circulation 2022 Feb 22;145(8):586-602.


dataset_id: SCDS0000039
title: Cell profiling of acute kidney injury reveals conserved cellular responses to injury
species: Mus musculus
tissues: Kidney
sex: Unknown
technologies: scRNA
disease: Acute kidney injury
overall_design: 10X Chromium was used to profile mouse AKI kidneys
submission_date: 2019-10-18 00:00:00
last_modified: 2024-07-03 00:00:00
contributors: Humphreys BD
contacts: humphreysbd@wustl.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139107
platforms: Illumina NovaSeq 6000
pmid: 32571916
has_paired: STDS0000121
summary:
  After acute kidney injury (AKI), patients either recover or alternatively develop fibrosis and chronic kidney disease. Interactions between injured epithelia, stroma and inflammatory cells determine whether kidneys repair or undergo fibrosis, but the molecular events that drive these processes are poorly understood. Here, we use single nucleus RNA sequencing of a mouse model of AKI to characterize cell states during repair from acute injury. We identify a distinct proinflammatory and profibrotic proximal tubule cell state that fails to repair. Deconvolution of bulk RNA-seq datasets indicates that this âfailed-repair proximal tubule cellâ or FR-PTC, state can be detected in other models of kidney injury, increasing in the aging rat kidney and over time in human kidney allografts. We also describe dynamic intercellular communication networks and discern transcriptional pathways driving successful vs. failed repair.  Our study provides a detailed description of cellular responses after injury and suggests that the FR-PTC state may represent a therapeutic target to improve repair.

citation:
  Kirita Y, Wu H, Uchimura K, Wilson PC et al. Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury. Proc Natl Acad Sci U S A 2020 Jul 7;117(27):15874-15883.


dataset_id: SCDS0000040
title: scRNA.Sequencing data [scRNA_Seq_SCC25]
species: Homo sapiens
sex: Unknown
technologies: scRNA
disease: Palmitic acid
submission_date: 2020-04-21 00:00:00
last_modified: 2021-11-16 00:00:00
contributors: DomÃ­nguez D,HernÃ¡ndez I,Heyn H,Aznar S
contacts: aberenguerl@tauli.cat
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149041
platforms: Illumina HiSeq 2500
pmid: 34759321
has_paired: STDS0000120
summary:
  Transcriptional profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal from the culture.

overall_design:
  single cell transcriptional profiling of CD44+ Live (Dapi-) i) 4 days untreated and 4 days palmitic acid (PA)-treated SCC-25 cells as well as ii) 14 days untreated and post 14 days PA treatment  SCC-25 cells

citation:
  Pascual G, Domínguez D, Elosúa-Bayes M, Beckedorff F et al. Dietary palmitic acid promotes a prometastatic memory via Schwann cells. Nature 2021 Nov;599(7885):485-490.


dataset_id: SCDS0000041
title: Single cell RNASeq of whole mouse kidneys from Uromodulin/Tamm horsfall protein knock-out mice
species: Mus musculus
tissues: Kidney
sex: Unknown
technologies: scRNA
disease: Acute kidney injury
submission_date: 2021-04-07 00:00:00
last_modified: 2021-12-01 00:00:00
contributors: Winfree S,El-Achkar TM
contacts: winfrees@iu.edu, swinfree@unmc.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171639
platforms: Illumina NovaSeq 6000
pmid: 34003797
has_paired: STDS0000007
summary:
  To elucidate changes in cellular populations in the ischemic acute kidney injury, we performed single cell RNAseq on mouse kidneys following ischemic reperfusion injury and a sham surgery.  Mice were subjected to bilateral clamping of the renal pedicule for 30 minutes.  After 6-7 hours of reperfusion the kidneys were removed and processed by a MACs cell isolation protocol and dead cell removal (PMID:33448928) , sorted on a 10X Chromium platform version 3 and libraries generated.  Sequencing was performed on an Illumina NovaSeq 6000.

overall_design:
  Uromodulin/Tamm horsfall protein knock-out 129ev mice were subjected to a Sham surgery or bilateral renal clamping for 30 minutes.

citation:
  Melo Ferreira R, Sabo AR, Winfree S, Collins KS et al. Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury. JCI Insight 2021 Jun 22;6(12).


dataset_id: SCDS0000042
species: Mus musculus
tissues: Brain
organ_parts: Olfactory bulb
sex: Unknown
technologies: scRNA
disease: Olfactory bulb
submission_date: 2018-10-29 00:00:00
last_modified: 2021-09-29 00:00:00
contributors: Hill MC,Martin JF,Arenkiel BR
contacts: mhill@broadinstitute.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121891
platforms: Illumina NextSeq 500
pmid: 30517858
has_paired: STDS0000107
title:
  Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons

summary:
  Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions.  Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis.  To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system.

overall_design:
  To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.

citation:
  Tepe B, Hill MC, Pekarek BT, Hunt PJ et al. Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons. Cell Rep 2018 Dec 4;25(10):2689-2703.e3.


dataset_id: SCDS0000043
title: Interleukin-17 governs hypoxic adaptation of injured epithelium [CITE-seq & single-cell RNA-seq]
species: Mus musculus
tissues: Skin
sex: Unknown
technologies: scRNA
disease: Skin injury
submission_date: 2021-02-17 00:00:00
last_modified: 2023-01-05 00:00:00
contributors: Konieczny P,Yue X,Sidhu I,Naik S
contacts: Shruti.Naik@nyulangone.org
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166949
platforms: Illumina HiSeq 4000
pmid: 35709248
has_paired: STDS0000089
summary:
  To define the composition of first responder lymphocytes that may engage in crosstalk with injured epithelium we profiled the lymphoytes from unwounded health skin and skin from different time points after wounding with CITE-seq and single-cell RNA-sequencing.

overall_design:
  Lymphocytes (CD45.2+ CD90.2+ TCR VÎ³3 - )from unwounded skin, 3, and 5 days post wounding were sorted based on surface marker staining. Cells were prelabeled with surface epitope marking oligo-tagged antibodies and sample specific oligo-tagged Totalseq-A antibodies (Biolegend, see table 1). Hashed samples were pooled for scRNA-seq with 10X Chromium 3' v3 platform. RUN1 and RUN2 represent technical replicates.

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: SCDS0000044
title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [single-cell RNA-seq]
species: Homo sapiens
tissues: Skin
sex: Unknown
technologies: scRNA
disease: Squamous carcinoma
submission_date: 2020-01-24 00:00:00
last_modified: 2022-05-02 00:00:00
contributors: Ji AL,Rubin AJ
contacts: andrew.ji@mssm.edu
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144236
platforms: Illumina HiSeq 4000
pmid: 32579974
has_paired: STDS0000001
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, normal skin, and tumor xenografts of human SCC cell lines in immunocompromised mice were dissociated into single-cell suspensions and scRNA-seq was performed with the 10X Chromium 3 v2 platform. A prior patient metadata file (patient_metadata.txt.gz) contained scrambled barcode names. An updated file (patient_metadata_new.txt.gz) is now corrected to match the counts matrix barcode names.

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: SCDS0000045
species: Homo sapiens
tissues: Cervical
organ_parts: Cervical tissue
sex: Unknown
technologies: scRNA
disease: N_HPV | HSIL_HPV | CA_HPV
submission_date: 2022-07-20 00:00:00
last_modified: 2023-12-01 00:00:00
contributors: Guo C
contacts: 13301050323@fudan.edu.cn
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208653
platforms: Illumina NovaSeq 6000
pmid: 36967539
has_paired: STDS0000113
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 [scRNA-seq]

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 âHPV-related epithelial clustersâ 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 âhomeostasis-balance-malignancyâ 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: STDS0000271
species: Solanum lycopersicum
cell_types: chlorenchyma cells
accessions: https://db.cngb.org/search/project/CNP0003986
pmid: 37703282
title:
  Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus

summary:
  Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.

contributors:
  Xiehai Song, Pengru Guo, Keke Xia, Meiling Wang, Yongqi Liu, Lichuan Chen, Jinhui Zhang, Mengyuan Xu, Naixu Liu, Zhiliang Yue, Xun Xu, Ying Gu, Gang Li, Min Liu, Liang Fang, Xing Wang Deng, Bosheng Li

citation:
  Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2310163120. doi: 10.1073/pnas.2310163120. Epub 2023 Sep 13. PMID: 37703282; PMCID: PMC10515167.


dataset_id: STDS0000272
species: Arabidopsis
cell_types: upper epidermal cells, lower epidermal cells, vascular cells, guard cells
accessions: https://db.cngb.org/stomics/datasets/STDS0000104
pmid: 35512702
title:
  The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

summary:
  Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biological functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single-cell location and transcriptome information for plant biology study.

contributors:
  Keke Xia, Hai-Xi Sun, Jie Li, Jiming Li, Yu Zhao, Lichuan Chen, Chao Qin, Ruiying Chen, Zhiyong Chen, Guangyu Liu, Ruilian Yin, Bangbang Mu, Xiaojuan Wang, Mengyuan Xu, Xinyue Li, Peisi Yuan, Yixin Qiao, 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 K, Sun HX, Li J, Li J, Zhao Y, Chen L, Qin C, Chen R, Chen Z, Liu G, Yin R, Mu B, Wang X, Xu M, Li X, Yuan P, Qiao Y, Hao S, Wang J, Xie Q, Xu J, Liu S, Li Y, Chen A, Liu L, Yin Y, Yang H, Wang J, Gu Y, Xu X. The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Dev Cell. 2022 May 23;57(10):1299-1310.e4. doi: 10.1016/j.devcel.2022.04.011. Epub 2022 May 4. PMID: 35512702.


dataset_id: STDS0000273
title: Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the peg
species: Arachis hypogaea (peanut)
pmid: 35792883
cell_types:
  Epidermis and exodermis, Cortex regions, Phloem parenchyma, xylem parenchyma, epidermis/exodermis, Cambium cells, xylem vessel, xylem parenchyma cells, sieve element-companion cells, Ovules

summary:
  High-throughput single-cell RNA sequencing (scRNA-seq) faces limitations in non-model species due to challenges in protoplasting and reliance on marker genes. This study introduces an improved Stereo-seq technology applied to peanut (Arachis hypogaea), focusing on the unique "peg" organ—a stem-like structure with root-like gravitropism. Using optimized cryo-embedding and permeabilization methods, the authors generated a high-resolution spatial transcriptome atlas across four peanut tissues (root, hypocotyl, stem, peg).
  The pipeline yielded 938 million clean reads, identifying 35,970–47,304 genes per tissue. Unsupervised clustering (Seurat/UMAP) revealed 18 distinct cell clusters, highlighting divergent gene expression in anatomically similar cells across tissues. For example, epidermis/exodermis clusters in stems/hypocotyls (Cluster11) split into subclusters enriched for photosynthesis (stems) and cell wall/disease resistance genes (hypocotyls). The peg’s tip (Cluster13) expressed genes linked to glycoside/saponin synthesis, while its base (Cluster2) showed environmental signal-sensing genes, aligning with its developmental roles.
  In the stem, nine clusters (S0–S8) mirrored anatomical features, with pseudo-time analysis tracing cambial cell differentiation into xylem/phloem lineages. Novel stress/disease resistance genes (e.g., RD22, BBI1) were spatially mapped, validated via qPCR and in situ hybridization.
  This study demonstrates Stereo-seq’s utility in non-model species, providing spatial transcriptomic insights without marker gene dependence. The atlas reveals cell heterogeneity and functional divergence in peanut, offering a framework for nanoscale functional genomics and future biological research in plants.

contributors:
  Yiyang Liu, Chunhua Li, Yan Han, Rongchong Li, Feng Cui, He Zhang, Xiaoshan Su, Xiawei Liu, Guoxin Xu, Shubo Wan, Guowei Li

citation:
  Liu Y, Li C, Han Y, Li R, Cui F, Zhang H, Su X, Liu X, Xu G, Wan S, Li G. Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the peg. Plant Biotechnol J. 2022 Sep;20(9):1648-1650. doi: 10.1111/pbi.13884. Epub 2022 Jul 23. PMID: 35792883; PMCID: PMC9398287.


dataset_id: STDS0000274
title: Spatial resolution of an integrated C4+CAM photosynthetic metabolism
species: Portulaca oleracea
cell_types: mesophyll cells
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA774250
pmid: 35930634
summary:
  C4 and CAM photosynthesis have repeatedly evolved in plants over the past 30 million years. Because both repurpose the same set of enzymes but differ in their spatial and temporal deployment, they have long been considered as distinct and incompatible adaptations. Portulaca contains multiple C4 species that perform CAM when droughted. Spatially explicit analyses of gene expression reveal that C4 and CAM systems are completely integrated in Portulaca oleracea, with CAM and C4 carbon fixation occurring in the same cells and CAM-generated metabolites likely incorporated directly into the C4 cycle. Flux balance analysis corroborates the gene expression findings and predicts an integrated C4+CAM system under drought. This first spatially explicit description of a C4+CAM photosynthetic metabolism presents a potential new blueprint for crop improvement.

contributors:
  Jose J Moreno-Villena, Haoran Zhou, Ian S Gilman, S Lori Tausta, C Y Maurice Cheung, Erika J Edwards

citation:
  Moreno-Villena JJ, Zhou H, Gilman IS, Tausta SL, Cheung CYM, Edwards EJ. Spatial resolution of an integrated C4+CAM photosynthetic metabolism. Sci Adv. 2022 Aug 5;8(31):eabn2349. doi: 10.1126/sciadv.abn2349. Epub 2022 Aug 5. PMID: 35930634; PMCID: PMC9355352.


dataset_id: STDS0000275
title: A spatiotemporal atlas of organogenesis in the development of orchid flowers
species: Phalaenopsis orchids
contributors: Chang Liu, Jing Leng, Yonglong Li, Tingting Ge, Jinglong Li, Yamao Chen, Chunce Guo, Ji Qi
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198128
pmid: 36095130
summary:
  Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.

citation:
  Liu C, Leng J, Li Y, Ge T, Li J, Chen Y, Guo C, Qi J. A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Res. 2022 Sep 23;50(17):9724-9737. doi: 10.1093/nar/gkac773. PMID: 36095130; PMCID: PMC9508851.


dataset_id: STDS0000276
species: Poplar
cell_types: rectangle shape procambium-like (PCL) cells, fusiform shape cambium zone (CZ) meristematic cells
contributors: Juan Du, Yichen Wang, Wenfan Chen, Mingling Xu, Ruhong Zhou, Huixia Shou, Jun Chen
accessions: https://db.cngb.org/stomics/datasets/STDS0000104
pmid: 36895162
title:
  High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem

summary:
  The secondary vascular tissue emanating from meristems is central to understanding how vascular plants such as forest trees evolve, grow, and regulate secondary radial growth. However, the overall molecular characterization of meristem origins and developmental trajectories from primary to secondary vascular tissues in woody tree stems is technically challenging. In this study, we combined high-resolution anatomic analysis with a spatial transcriptome (ST) technique to define features of meristematic cells in a developmental gradient from primary to secondary vascular tissues in poplar stems. The tissue-specific gene expression of meristems and derived vascular tissue types were accordingly mapped to specific anatomical domains. Pseudotime analyses were used to track the origins and changes of meristems throughout the development from primary to secondary vascular tissues. Surprisingly, two types of meristematic-like cell pools within secondary vascular tissues were inferred based on high-resolution microscopy combined with ST, and the results were confirmed by in situ hybridization of, transgenic trees, and single-cell sequencing. The rectangle shape procambium-like (PCL) cells develop from procambium meristematic cells and are located within the phloem domain to produce phloem cells, whereas fusiform shape cambium zone (CZ) meristematic cells develop from fusiform metacambium meristematic cells and are located inside the CZ to produce xylem cells. The gene expression atlas and transcriptional networks spanning the primary transition to secondary vascular tissues generated in this work provide new resources for studying the regulation of meristem activities and the evolution of vascular plants. A web server (https://pgx.zju.edu.cn/stRNAPal/) was also established to facilitate the use of ST RNA-seq data.

citation:
  Du J, Wang Y, Chen W, Xu M, Zhou R, Shou H, Chen J. High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem. Mol Plant. 2023 May 1;16(5):809-828. doi: 10.1016/j.molp.2023.03.005. Epub 2023 Mar 9. PMID: 36895162.


dataset_id: STDS0000277
species: Legumes, Rhizobium
cell_types: uninfected cells, infected cells, transitional subtype of infected cells
accessions: https://ngdc.cncb.ac.cn/omix/release/OMIX002290
pmid: 37055554
title:
  Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

summary:
  Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.

contributors:
  Zhijian Liu, Xiangying Kong, Yanping Long, Sirui Liu, Hong Zhang, Jinbu Jia, Wenhui Cui, Zunmian Zhang, Xianwei Song, Lijuan Qiu, Jixian Zhai, Zhe Yan

citation:
  Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z. Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Nat Plants. 2023 Apr;9(4):515-524. doi: 10.1038/s41477-023-01387-z. Epub 2023 Apr 13. PMID: 37055554.


dataset_id: STDS0000278
title: Spatial metatranscriptomics resolves host-bacteria-fungi interactomes
species: Arabidopsis thaliana, Homo sapiens
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA784452
pmid: 37985875
summary:
  The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks and spatial patterns. Existing technology does not allow the simultaneous investigation of spatial interactions between a host and the multitude of its colonizing microorganisms, which limits our understanding of host-microorganism interactions within a plant or animal tissue. Here we present spatial metatranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and find tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intrakingdom spatial interactions among microorganisms, as well as the host response to microbial hotspots. SmT provides an approach for answering fundamental questions on host-microbiome interplay.

contributors:
  Sami Saarenpää, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek Severi Lundberg, Detlef Weigel, Stefania Giacomello

citation:
  Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Lundberg DS, Weigel D, Giacomello S. Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nat Biotechnol. 2024 Sep;42(9):1384-1393. doi: 10.1038/s41587-023-01979-2. Epub 2023 Nov 20. PMID: 37985875; PMCID: PMC11392817.


dataset_id: STDS0000279
title: Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development
species: Zea mays
cell_types: 11 cell populations
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1031340
pmid: 37938556
summary:
  Maize kernels are complex biological systems composed of three genetic sources, namely maternal tissues, progeny embryos, and progeny endosperms. The lack of gene expression profiles with spatial information has limited the understanding of the specific functions of each cell population, and hindered the exploration of superior genes in kernels. In our study, we conduct microscopic sectioning and spatial transcriptomics analysis during the grain filling stage of maize kernels. This enables us to visualize the expression patterns of all genes through electronical RNA in situ hybridization, and identify 11 cell populations and 332 molecular marker genes. Furthermore, we systematically elucidate the spatial storage mechanisms of the three major substances in maize kernels: starch, protein, and oil. These findings provide valuable insights into the functional genes that control agronomic traits in maize kernels.

contributors:
  Yuxin Fu, Wenxin Xiao, Lang Tian, Liangxing Guo, Guangjin Ma, Chen Ji, Yongcai Huang, Haihai Wang, Xingguo Wu, Tao Yang, Jiechen Wang, Jirui Wang, Yongrui Wu, Wenqin Wang

citation:
  Fu Y, Xiao W, Tian L, Guo L, Ma G, Ji C, Huang Y, Wang H, Wu X, Yang T, Wang J, Wang J, Wu Y, Wang W. Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development. Nat Commun. 2023 Nov 8;14(1):7191. doi: 10.1038/s41467-023-43006-7. Erratum in: Nat Commun. 2024 Jan 4;15(1):279. doi: 10.1038/s41467-023-44536-w. PMID: 37938556; PMCID: PMC10632454.


dataset_id: STDS0000280
species: Populus
cell_types: cambium, xylem precursors, phloem precursors, vessel, fiber
contributors: Renhui Li, Zhifeng Wang, Jia-Wei Wang, Laigeng Li
accessions: https://ngdc.cncb.ac.cn/gsa/browse/CRA010013
pmid: 37491818
title:
  Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees

summary:
  Primary and secondary growth of the tree stem are responsible for corresponding increases in trunk height and diameter. However, our molecular understanding of the biological processes that underlie these two types of growth is incomplete. In this study, we used single-cell RNA sequencing and spatial transcriptome sequencing to reveal the transcriptional landscapes of primary and secondary growth tissues in the Populus stem. Comparison between the cell atlas and differentiation trajectory of primary and secondary growth revealed different regulatory networks involved in cell differentiation from cambium to xylem precursors and phloem precursors. These regulatory networks may be controlled by auxin accumulation and distribution. Analysis of cell differentiation trajectories suggested that vessel and fiber development followed a sequential pattern of progressive transcriptional regulation. This research provides new insights into the processes of cell identity and differentiation that occur throughout primary and secondary growth of tree stems, increasing our understanding of the cellular differentiation dynamics that occur during stem growth in trees.

citation:
  Li R, Wang Z, Wang JW, Li L. Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees. Plant Commun. 2023 Sep 11;4(5):100665. doi: 10.1016/j.xplc.2023.100665. Epub 2023 Jul 24. PMID: 37491818; PMCID: PMC10504605.


dataset_id: STDS0000281
title: Spatial transcriptomics of a lycophyte root sheds light on root evolution
species: Selaginella moellendorffii, Arabidopsis, Ceratopteris richardii
cell_types: root cap cells
accessions: https://bioinformatics.psb.ugent.be/webtools/spatial-transcriptomics/selaginella/
pmid: 37683643
summary:
  Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.

contributors:
  Xilan Yang, Ward Poelmans, Carolin Grones, Abdellah Lakehal, Julie Pevernagie, Michiel Van Bel, Maria Njo, Lin Xu, Hilde Nelissen, Bert De Rybel, Hans Motte, Tom Beeckman

citation:
  Yang X, Poelmans W, Grones C, Lakehal A, Pevernagie J, Van Bel M, Njo M, Xu L, Nelissen H, De Rybel B, Motte H, Beeckman T. Spatial transcriptomics of a lycophyte root sheds light on root evolution. Curr Biol. 2023 Oct 9;33(19):4069-4084.e8. doi: 10.1016/j.cub.2023.08.030. Epub 2023 Sep 7. PMID: 37683643.


dataset_id: STDS0000282
title: Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination
species: Oryza sativa
cell_types: two unreported scutellum cell types
pmid: 38848718
summary:
  Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.

contributors:
  Jie Yao, Qinjie Chu, Xing Guo, Wenwen Shao, Nianmin Shang, Kang Luo, Xiaohan Li, Hongyu Chen, Qing Cheng, Fangyu Mo, Dihuai Zheng, Fan Xu, Fu Guo, Qian-Hao Zhu, Shuiguang Deng, Chengcai Chu, Xun Xu, Huan Liu, Longjiang Fan

citation:
  Yao J, Chu Q, Guo X, Shao W, Shang N, Luo K, Li X, Chen H, Cheng Q, Mo F, Zheng D, Xu F, Guo F, Zhu QH, Deng S, Chu C, Xu X, Liu H, Fan L. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. Dev Cell. 2024 Sep 9;59(17):2320-2332.e5. doi: 10.1016/j.devcel.2024.05.016. Epub 2024 Jun 6. PMID: 38848718.


dataset_id: STDS0000283
title: A spatial transcriptome map of the developing maize ear
species: Maize
cell_types: 4 newly defined cell types found mainly in the inflorescence meristem
accessions: https://db.cngb.org/search/project/CNP0004249/
pmid: 38745100
summary:
  A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging owing to a lack of specific marker genes to distinguish among cell types, particularly in different types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of the developing maize ear primordium, identifying 12 cell types, including 4 newly defined cell types found mainly in the inflorescence meristem. By extracting the meristem components for detailed clustering, we identified three subtypes of meristem and validated two MADS-box genes that were specifically expressed at the apex of determinate meristems and involved in stem cell determinacy. Furthermore, by integrating single-cell RNA transcriptomes, we identified a series of spatially specific networks and hub genes that may provide new insights into the formation of different tissues. In summary, this study provides a valuable resource for research on cereal inflorescence development, offering new clues for yield improvement.

contributors:
  Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David Jackson, Zuxin Zhang, Xun Xu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang

citation:
  Wang Y, Luo Y, Guo X, Li Y, Yan J, Shao W, Wei W, Wei X, Yang T, Chen J, Chen L, Ding Q, Bai M, Zhuo L, Li L, Jackson D, Zhang Z, Xu X, Yan J, Liu H, Liu L, Yang N. A spatial transcriptome map of the developing maize ear. Nat Plants. 2024 May;10(5):815-827. doi: 10.1038/s41477-024-01683-2. Epub 2024 May 14. PMID: 38745100.


dataset_id: STDS0000284
title: Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple
species: Ananas comosus
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA305042
pmid: 28670834
summary:
  The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in an up to 80% higher water-use efficiency than C3 photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA (miRNA) expression patterns in the obligate CAM plant pineapple [Ananas comosus (L.) Merr.]. The high-resolution transcriptome atlas allowed us to distinguish between CAM-related and non-CAM gene copies. A differential gene co-expression network across green and white leaf diel datasets identified genes with circadian oscillation, CAM-related functions, and source-sink relations. Gene co-expression clusters containing CAM pathway genes are enriched with clock-associated cis-elements, suggesting circadian regulation of CAM. About 20% of pineapple microRNAs have diel expression patterns, with several that target key CAM-related genes. Expression and physiology data provide a model for CAM-specific carbohydrate flux and long-distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering of CAM into C3 photosynthesis crop species.

contributors:
  Ching M Wai, Robert VanBuren, Jisen Zhang, Lixian Huang, Wenjing Miao, Patrick P Edger, Won C Yim, Henry D Priest, Blake C Meyers, Todd Mockler, J Andrew C Smith, John C Cushman, Ray Ming

citation:
  Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger PP, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. Plant J. 2017 Oct;92(1):19-30. doi: 10.1111/tpj.13630. Epub 2017 Aug 21. PMID: 28670834.


dataset_id: STDS0000285
title: The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer
species: Asian ginseng, American ginseng
contributors: Kangyu Wang, Shicui Jiang, Chunyu Sun, Yanping Lin, Rui Yin, Yi Wang, Meiping Zhang
pmid: 26655864
summary:
  Ginseng, including Asian ginseng (Panax ginseng C. A. Meyer) and American ginseng (P. quinquefolius L.), is one of the most important medicinal herbs in Asia and North America, but significantly understudied. This study sequenced and characterized the transcriptomes and expression profiles of genes expressed in 14 tissues and four different aged roots of Asian ginseng. A total of 265.2 million 100-bp clean reads were generated using the high-throughput sequencing platform HiSeq 2000, representing >8.3x of the 3.2-Gb ginseng genome. From the sequences, 248,993 unigenes were assembled for whole plant, 61,912-113,456 unigenes for each tissue and 54,444-65,412 unigenes for different year-old roots. We comprehensively analyzed the unigene sets and gene expression profiles. We found that the number of genes allocated to each functional category is stable across tissues or developmental stages, while the expression profiles of different genes of a gene family or involved in ginsenoside biosynthesis dramatically diversified spatially and temporally. These results provide an overall insight into the spatial and temporal transcriptome dynamics and landscapes of Asian ginseng, and comprehensive resources for advanced research and breeding of ginseng and related species.

citation:
  Wang K, Jiang S, Sun C, Lin Y, Yin R, Wang Y, Zhang M. The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer. Sci Rep. 2015 Dec 11;5:18283. doi: 10.1038/srep18283. PMID: 26655864; PMCID: PMC4675998.


dataset_id: STDS0000286
species: Rhododendron decorum Franch.
cell_types: leaves, corollas, androecium/gynoecium
contributors: Weiwei Liu, Chenghua Yu, Kaiye Yang, Ling Wang, Zhongyu Fan, Xinchun Mo
pmid: 39596682
title:
  Comparative and Spatial Transcriptome Analysis of Rhododendron decorum Franch. During the Flowering Period and Revelation of the Plant Defense Mechanism

summary:
  Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized by local communities for its medicinal and edible properties. However, the transcriptional regulation function, medicinal properties, and edibility characteristics of R. decorum Franch. currently lack a solid theoretical basis.Methods: Total RNA was extracted from leaves, corollas and androecium/gynoecium of R. decorum Franch. in Heqing county, followed by the construction of cDNA libraries and the de novo assembly of transcriptomes.Results: A total of 63,050 unigenes were extracted from the flowers and leaf organs of R. decorum Franch. Among these unigenes, 43,517 were predicted to be coding sequences, with 32,690 being effectively annotated. Differential gene expression enrichment was observed among different organs within their respective transcriptomes; notably floral organs exhibited significant defense against plant diseases along with signal transduction functions. Furthermore, during the flower harvesting period, all floral organs exhibited gene enrichment pathways associated with carbohydrate metabolism. Additionally, the stamen and pistil displayed flavonoid metabolism pathways, suggesting their potential applications as functional food or medicine.Conclusions: Our results shed light on plant-pathogen defense mechanisms and the molecular bias of flavonoids biosynthesis on flower organs during the flowering period, which might help to understand the consumption of R. decorum Franch. corollas by the Bai nationality of Heqing county.

citation:
  Liu W, Yu C, Yang K, Wang L, Fan Z, Mo X. Comparative and Spatial Transcriptome Analysis of Rhododendron decorum Franch. During the Flowering Period and Revelation of the Plant Defense Mechanism. Genes (Basel). 2024 Nov 18;15(11):1482. doi: 10.3390/genes15111482. PMID: 39596682; PMCID: PMC11593350.


dataset_id: STDS0000287
title: Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics
species: Mus musculus, Homo sapiens
organ_parts: brain
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217058
pmid: 37143153
summary:
  Background: Rhynchophylline (RHY) is an alkaloid component of Uncaria, which are plants extensively used in traditional Asian medicines. Uncaria treatments increase sleep time and quality in humans, and RHY induces sleep in rats. However, like many traditional natural treatments, the mechanisms of action of RHY and Uncaria remain evasive. Moreover, it is unknown whether RHY modifies key brain oscillations during sleep. We thus aimed at defining the effects of RHY on sleep architecture and oscillations throughout a 24-h cycle, as well as identifying the underlying molecular mechanisms. Mice received systemic RHY injections at two times of the day (beginning and end of the light period), and vigilance states were studied by electrocorticographic recordings.Results: RHY enhanced slow wave sleep (SWS) after both injections, suppressed paradoxical sleep (PS) in the light but enhanced PS in the dark period. Furthermore, RHY modified brain oscillations during both wakefulness and SWS (including delta activity dynamics) in a time-dependent manner. Interestingly, most effects were larger in females. A brain spatial transcriptomic analysis showed that RHY modifies the expression of genes linked to cell movement, apoptosis/necrosis, and transcription/translation in a brain region-independent manner, and changes those linked to sleep regulation (e.g., Hcrt, Pmch) in a brain region-specific manner (e.g., in the hypothalamus).Conclusions: The findings provide support to the sleep-inducing effect of RHY, expose the relevance to shape wake/sleep oscillations, and highlight its effects on the transcriptome with a high spatial resolution. The exposed molecular mechanisms underlying the effect of a natural compound should benefit sleep- and brain-related medicine.

contributors:
  Maria Neus Ballester Roig, Tanya Leduc, Julien Dufort-Gervais, Yousra Maghmoul, Olivier Tastet, Valérie Mongrain

citation:
  Ballester Roig MN, Leduc T, Dufort-Gervais J, Maghmoul Y, Tastet O, Mongrain V. Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics. Biol Direct. 2023 May 5;18(1):21. doi: 10.1186/s13062-023-00377-7. PMID: 37143153; PMCID: PMC10161643.


dataset_id: STDS0000288
title: Spatial transcriptomes of iron-deficient and cadmium-stressed rice
species: Oryza sativa
cell_types: vascular bundle, cortex, epidermis plus exodermis
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40549
pmid: 24188410
summary:
  Although the genes involved in metal homeostasis have been investigated over the past few decades, many genes related to metal homeostasis remain uncharacterized, and a comprehensive analysis of the expression of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed Oryza sativa (rice) using laser microdissection and microarray analysis. Roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle, cortex, and epidermis plus exodermis. In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately. The spatial expression patterns were distinct in each tissue type. Fe deficiency and Cd stress also had significant effects on the transcriptomes, although these were less pronounced than the spatial effects. Genes encoding transporters involved in metal homeostasis, proteins associated with heavy metal detoxification, and phytohormone-related proteins were comprehensively investigated. Additionally, cis motifs involved in the regulation of these diverse expression changes in various tissue types were predicted. The spatial transcriptomes presented here provide novel insight into the molecular mechanisms of metal homeostasis.

contributors:
  Yuko Ogo, Yusuke Kakei, Reiko Nakanishi Itai, Takanori Kobayashi, Hiromi Nakanishi, Hirokazu Takahashi, Mikio Nakazono, Naoko K Nishizawa

citation:
  Ogo Y, Kakei Y, Itai RN, Kobayashi T, Nakanishi H, Takahashi H, Nakazono M, Nishizawa NK. Spatial transcriptomes of iron-deficient and cadmium-stressed rice. New Phytol. 2014 Feb;201(3):781-794. doi: 10.1111/nph.12577. Epub 2013 Nov 5. PMID: 24188410.


dataset_id: STDS0000289
species: Arabidopsis thaliana, Botrytis cinerea
contributors: Joseph M K Mulema, Katherine J Denby
pmid: 21785916
title:
  Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction

summary:
  Plants activate an array of defence responses following recognition of pathogenic organisms. This study attempted to characterize at a transcriptional level, the defence responses of Arabidopsis thaliana after infection with Botrytis cinerea using microarrays. Alteration in transcript levels following infection was investigated in time (temporal) and space (spatial). A number of genes were up- and down-regulated specifically at 12 h, others at 24 h while others were up- and down-regulated at both time points. Similarly, some genes were specifically induced very close to the lesion while others in more distal tissue. Clustering of expression profiles resulting from other biotic and abiotic interactions with Arabidopsis indicated a large overlap in gene expression. This study highlighted a multitude of genes induced in Arabidopsis spatially and temporally following infection with B. cinerea providing an insight into key processes of defence against this pathogen. The plethora of altered genes identified are candidates for further investigation.

citation:
  Mulema JM, Denby KJ. Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction. Mol Biol Rep. 2012 Apr;39(4):4039-49. doi: 10.1007/s11033-011-1185-4. Epub 2011 Jul 23. PMID: 21785916.


dataset_id: STDS0000290
species: Prunus species
pmid: 34842310
title:
  The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome

summary:
  Genome-wide transcriptome analysis provides systems-level insights into plant biology. Due to the limited depth of quantitative proteomics our understanding of gene-protein-complex stoichiometry is largely unknown in plants. Recently, the complexity of the proteome and its cell-/tissue-specific distribution have boosted the research community to the integration of transcriptomics and proteomics landscapes in a proteogenomic approach. Herein, we generated a quantitative proteome and transcriptome abundance atlas of 15 major sweet cherry (Prunus avium L., cv 'Tragana Edessis') tissues represented by 29 247 genes and 7584 proteins. Additionally, 199 984 alternative splicing events, particularly exon skipping and alternative 3' splicing, were identified in 23 383 transcribed regions of the analyzed tissues. Common signatures as well as differences between mRNA and protein quantities, including genes encoding transcription factors and allergens, within and across the different tissues are reported. Using our integrated dataset, we identified key putative regulators of fruit development, notably genes involved in the biosynthesis of anthocyanins and flavonoids. We also provide proteogenomic-based evidence for the involvement of ethylene signaling and pectin degradation in cherry fruit ripening. Moreover, clusters of genes and proteins with similar and different expression and suppression trends across diverse tissues and developmental stages revealed a relatively low RNA abundance-to-protein correlation. The present proteogenomic analysis allows us to identify 17 novel sweet cherry proteins without prior protein-level annotation evidenced in the currently available databases. To facilitate use by the community, we also developed the Sweet Cherry Atlas Database (https://grcherrydb.com/) for viewing and data mining these resources. This work provides new insights into the proteogenomics workflow in plants and a rich knowledge resource for future investigation of gene and protein functions in Prunus species.

contributors:
  Aliki Xanthopoulou, Theodoros Moysiadis, Christos Bazakos, Evangelos Karagiannis, Ioanna Karamichali, George Stamatakis, Martina Samiotaki, Maria Manioudaki, Michail Michailidis, Panagiotis Madesis, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou

citation:
  Xanthopoulou A, Moysiadis T, Bazakos C, Karagiannis E, Karamichali I, Stamatakis G, Samiotaki M, Manioudaki M, Michailidis M, Madesis P, Ganopoulos I, Molassiotis A, Tanou G. The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome. Plant J. 2022 Mar;109(5):1319-1336. doi: 10.1111/tpj.15612. Epub 2021 Dec 16. PMID: 34842310.


dataset_id: STDS0000291
title: Putting genes on the map: Spatial transcriptomics of the maize shoot apical meristem
species: Maize (Zea mays), Arabidopsis thaliana
contributors: Wei Zhang
pmid: 35355051
summary:
  The article explores the role of the shoot apical meristem (SAM) in plant development, focusing on maize (Zea mays). Plants, unlike animals, can continuously generate new organs due to pluripotent stem cells in the SAM, which coordinates stem cell maintenance and organogenesis. While single-cell transcriptomics provides gene expression data, spatial transcriptomics is needed to map gene expression in tissue context. Laureyns et al. (2021) optimized in situ sequencing to create a spatial transcriptome map of the maize SAM, identifying key genes like PLASTOCHRON1 (PLA1) involved in cell fate determination. The study validated the method's reliability, resolution, and specificity, revealing PLA1's role in defining indeterminate and determinate cell patterns. Future work should address sensitivity and resolution challenges in applying this approach to other plant organs and species, enhancing our understanding of cell and tissue organization.

citation:
  Zhang W. Putting genes on the map: Spatial transcriptomics of the maize shoot apical meristem. Plant Physiol. 2022 Mar 28;188(4):1931-1932. doi: 10.1093/plphys/kiab601. PMID: 35355051; PMCID: PMC8968254.


dataset_id: STDS0000292
title: Spatially resolved transcriptomic analysis of the germinating barley grain
species: Barley
cell_types: embryo, seedling
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218970
pmid: 37351575
summary:
  Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

contributors:
  Marta Peirats-Llobet, Changyu Yi, Lim Chee Liew, Oliver Berkowitz, Reena Narsai, Mathew G Lewsey, James Whelan

citation:
  Peirats-Llobet M, Yi C, Liew LC, Berkowitz O, Narsai R, Lewsey MG, Whelan J. Spatially resolved transcriptomic analysis of the germinating barley grain. Nucleic Acids Res. 2023 Aug 25;51(15):7798-7819. doi: 10.1093/nar/gkad521. PMID: 37351575; PMCID: PMC10450182.


dataset_id: STDS0000293
species: Lotus japonicus
accessions: https://db.cngb.org/search/project/CNP0004336
pmid: 39080318
title:
  Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics

summary:
  Legumes acquire nitrogen-fixing ability by forming root nodules. Transferring this capability to more crops could reduce our reliance on nitrogen fertilizers, thereby decreasing environmental pollution and agricultural production costs. Nodule organogenesis is complex, and a comprehensive transcriptomic atlas is crucial for understanding the underlying molecular events. Here, we utilized spatial transcriptomics to investigate the development of nodules in the model legume, Lotus japonicus. Our investigation has identified the developmental trajectories of two critical regions within the nodule: the infection zone and peripheral tissues. We reveal the underlying biological processes and provide gene sets to achieve symbiosis and material exchange, two essential aspects of nodulation. Among the candidate regulatory genes, we illustrate that LjNLP3, a transcription factor belonging to the NIN-LIKE PROTEIN family, orchestrates the transition of nodules from the differentiation to maturation. In summary, our research advances our understanding of nodule organogenesis and provides valuable data for developing symbiotic nitrogen-fixing crops.

contributors:
  Keyi Ye, Fengjiao Bu, Liyuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xueyong Yang, Xun Xu, Ertao Wang, William J Lucas, Sanwen Huang, Huan Liu, Jianshu Zheng

citation:
  Ye K, Bu F, Zhong L, Dong Z, Ma Z, Tang Z, Zhang Y, Yang X, Xu X, Wang E, Lucas WJ, Huang S, Liu H, Zheng J. Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics. Nat Commun. 2024 Jul 29;15(1):6387. doi: 10.1038/s41467-024-50737-8. PMID: 39080318; PMCID: PMC11289483.


dataset_id: STDS0000294
species: Hordeum vulgare
contributors: Alina Klaus, Caroline Marcon, Frank Hochholdinger
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA988922
pmid: 38243200
title:
  Spatiotemporal transcriptomic plasticity in barley roots: unravelling water deficit responses in distinct root zones

summary:
  Background: Drought poses a major threat to agricultural production and thus food security. Understanding the processes shaping plant responses to water deficit is essential for global food safety. Though many studies examined the effect of water deficit on the whole-root level, the distinct functions of each root zone and their specific stress responses remain masked by this approach.Results: In this study, we investigated the effect of water deficit on root development of the spring barley (Hordeum vulgare L.) cultivar Morex and examined transcriptomic responses at the level of longitudinal root zones. Water deficit significantly reduced root growth rates after two days of treatment. RNA-sequencing revealed root zone and temporal gene expression changes depending on the duration of water deficit treatment. The majority of water deficit-regulated genes were unique for their respective root zone-by-treatment combination, though they were associated with commonly enriched gene ontology terms. Among these, we found terms associated with transport, detoxification, or cell wall formation affected by water deficit. Integration of weighted gene co-expression analyses identified differential hub genes, that highlighted the importance of modulating energy and protein metabolism and stress response.Conclusion: Our findings provide new insights into the highly dynamic and spatiotemporal response cascade triggered by water deficit and the underlying genetic regulations on the level of root zones in the barley cultivar Morex, providing potential targets to enhance plant resilience against environmental constraints. This study further emphasizes the importance of considering spatial and temporal resolution when examining stress responses.

citation:
  Klaus A, Marcon C, Hochholdinger F. Spatiotemporal transcriptomic plasticity in barley roots: unravelling water deficit responses in distinct root zones. BMC Genomics. 2024 Jan 19;25(1):79. doi: 10.1186/s12864-024-10002-0. PMID: 38243200; PMCID: PMC10799489.


dataset_id: STDS0000295
species: Bamboo
cell_types: intercalary meristem cells, procambium cells, vascular tissue cells
contributors: Jing Guo, Dan Luo, Yamao Chen, Fengjiao Li, Jiajia Gong, Fen Yu, Wengen Zhang, Ji Qi, Chunce Guo
pmid: 39140996
title:
  Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots

summary:
  Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.

citation:
  Guo J, Luo D, Chen Y, Li F, Gong J, Yu F, Zhang W, Qi J, Guo C. Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots. New Phytol. 2024 Nov;244(3):1057-1073. doi: 10.1111/nph.20059. Epub 2024 Aug 14. PMID: 39140996.


dataset_id: STDS0000296
species: Zebrafish
accessions: https://db.cngb.org/stomics/zesta/download/
pmid: 35512701
title:
  Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

summary:
  A major challenge in understanding vertebrate embryogenesis 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 to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 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. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

contributors:
  Chang Liu, Rui Li, Young Li, Xiumei Lin, Kaichen Zhao, Qun Liu, Shuowen Wang, Xueqian Yang, Xuyang Shi, Yuting Ma, Chenyu Pei, Hui Wang, Wendai Bao, Junhou Hui, Tao Yang, Zhicheng Xu, Tingting Lai, Michael Arman Berberoglu, Sunil Kumar Sahu, Miguel A Esteban, Kailong Ma, Guangyi Fan, Yuxiang Li, Shiping Liu, Ao Chen, Xun Xu, Zhiqiang Dong, Longqi Liu

citation:
  Liu C, Li R, Li Y, Lin X, Zhao K, Liu Q, Wang S, Yang X, Shi X, Ma Y, Pei C, Wang H, Bao W, Hui J, Yang T, Xu Z, Lai T, Berberoglu MA, Sahu SK, Esteban MA, Ma K, Fan G, Li Y, Liu S, Chen A, Xu X, Dong Z, Liu L. Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. Dev Cell. 2022 May 23;57(10):1284-1298.e5. doi: 10.1016/j.devcel.2022.04.009. Epub 2022 May 4. PMID: 35512701.


dataset_id: STDS0000297
species: Salmo salar
organ_parts: filet, muscle
contributors: H Bjørgen, S Malik, E Rimstad, M Vaadal, I B Nyman, E O Koppang, T Tengs
pmid: 38087072
title:
  Cellular heterogeneity in red and melanized focal muscle changes in farmed Atlantic salmon (Salmo salar) visualized by spatial transcriptomics

summary:
  Spatial transcriptomics is a technique that provides insight into gene expression profiles in tissue sections while retaining structural information. We have employed this method to study the pathological conditions related to red and melanized focal changes in farmed Atlantic salmon (Salmo salar). Our findings support a model where similar molecular mechanisms are involved in both red and melanized filet discolorations and genes associated with several relevant pathways show distinct expression patterns in both sample types. Interestingly, there appears to be significant cellular heterogeneity in the foci investigated when looking at gene expression patterns. Some of the genes that show differential spatial expression are involved in cellular processes such as hypoxia and immune responses, providing new insight into the nature of muscle melanization in Atlantic salmon.

citation:
  Bjørgen H, Malik S, Rimstad E, Vaadal M, Nyman IB, Koppang EO, Tengs T. Cellular heterogeneity in red and melanized focal muscle changes in farmed Atlantic salmon (Salmo salar) visualized by spatial transcriptomics. Cell Tissue Res. 2024 Feb;395(2):199-210. doi: 10.1007/s00441-023-03850-x. Epub 2023 Dec 13. Erratum in: Cell Tissue Res. 2024 Feb;395(2):221. doi: 10.1007/s00441-023-03856-5. PMID: 38087072; PMCID: PMC10837230.


dataset_id: STDS0000298
title: Spatially resolved transcriptomic profiling of placental development in dairy cow
species: Ruminant animals, Homo sapiens
cell_types: uninucleate (UNC), binucleate (BNC) cells
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1093563
pmid: 38766743
summary:
  The placenta plays a crucial role in successful mammalian reproduction. Ruminant animals possess a semi-invasive placenta characterized by a highly vascularized structure formed by maternal endometrial caruncles and fetal placental cotyledons, essential for full-term fetal development. The cow placenta harbors at least two trophoblast cell populations: uninucleate (UNC) and binucleate (BNC) cells. However, the limited capacity to elucidate the transcriptomic dynamics of the placental natural environment has resulted in a poor understanding of both the molecular and cellular interactions between trophoblast cells and niches, and the molecular mechanisms governing trophoblast differentiation and functionalization. To fill this knowledge gap, we employed Stereo-seq to map spatial gene expression patterns at near single-cell resolution in the cow placenta at 90 and 130 days of gestation, attaining high-resolution, spatially resolved gene expression profiles. Based on clustering and cell marker gene expression analyses, key transcription factors, including YBX1 and NPAS2, were shown to regulate the heterogeneity of trophoblast cell subpopulations. Cell communication and trajectory analysis provided a framework for understanding cell-cell interactions and the differentiation of trophoblasts into BNCs in the placental microenvironment. Differential analysis of cell trajectories identified a set of genes involved in regulation of trophoblast differentiation. Additionally, spatial modules and co-variant genes that help shape specific tissue structures were identified. Together, these findings provide foundational insights into important biological pathways critical to the placental development and function in cows.

contributors:
  Guang-Hui Tan, Shi-Jie Liu, Ming-Le Dou, De-Feng Zhao, Ao Zhang, Heng-Kuan Li, Fu-Nong Luo, Tao Shi, Hao-Ping Wang, Jing-Yuan Lei, Yong Zhang, Yu Jiang, Yi Zheng, Fei Wang

citation:
  Tan GH, Liu SJ, Dou ML, Zhao DF, Zhang A, Li HK, Luo FN, Shi T, Wang HP, Lei JY, Zhang Y, Jiang Y, Zheng Y, Wang F. Spatially resolved transcriptomic profiling of placental development in dairy cow. Zool Res. 2024 May 18;45(3):586-600. doi: 10.24272/j.issn.2095-8137.2023.205. PMID: 38766743; PMCID: PMC11188604.


dataset_id: STDS0000299
species: Planarians
cell_types: pluripotent neoblast subtype
accessions: https://ngdc.cncb.ac.cn/gsa/browse/CRA007941
pmid: 37268637
title:
  Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration

summary:
  Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.

contributors:
  Guanshen Cui, Kangning Dong, Jia-Yi Zhou, Shang Li, Ying Wu, Qinghua Han, Bofei Yao, Qunlun Shen, Yong-Liang Zhao, Ying Yang, Jun Cai, Shihua Zhang, Yun-Gui Yang

citation:
  Cui G, Dong K, Zhou JY, Li S, Wu Y, Han Q, Yao B, Shen Q, Zhao YL, Yang Y, Cai J, Zhang S, Yang YG. Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration. Nat Commun. 2023 Jun 2;14(1):3205. doi: 10.1038/s41467-023-39016-0. PMID: 37268637; PMCID: PMC10238425.


dataset_id: STDS0000300
species: Rabbits
organ_parts: rabbit brains, intracranial arteries, intracranial veins
cell_types: smooth muscle cells
contributors: Matthew S Zabriskie, Daniel L Cooke, Chuanzhuo Wang, Matthew D Alexander
pmid: 35306920
title:
  Spatially resolved transcriptomics for evaluation of intracranial vessels in a rabbit model: Proof of concept

summary:
  Background: Better understanding of vessel biology and vascular pathophysiology is needed to improve understanding of cerebrovascular disorders. Tissue from diseased vessels can offer the best data. Rabbit models can be effective for studying intracranial vessels, filling gaps resulting from difficulties acquiring human tissue. Spatially-resolved transcriptomics (SRT) in particular hold promise for studying such models as they build on RNA sequencing methods, augmenting such data with histopathology.Methods: Rabbit brains with intact arteries were flash frozen, cryosectioned, and stained with H&E to confirm adequate inclusion of intracranial vessels before proceeding with tissue optimization and gene expression analysis using the Visium SRT platform. SRT results were analyzed with k-means clustering analysis, and differential gene expression was examined, comparing arteries to veins.Results: Cryosections were successfully mounted on Visium proprietary slides. Quality control thresholds were met. Optimum permeabilization was determined to be 24 min for the tissue optimization step. In analysis of SRT data, k-means clustering distinguished vascular tissue from parenchyma. When comparing gene expression traits, the most differentially expressed genes were those found in smooth muscle cells. These genes were more commonly expressed in arteries compared to veins.Conclusions: Intracranial vessels from model rabbits can be processed and analyzed with the Visium SRT platform. Face validity is found in the ability of SRT data to distinguish vessels from parenchymal tissue and differential expression analysis accurately distinguishing arteries from veins. SRT should be considered for future animal model investigations into cerebrovascular diseases.

citation:
  Zabriskie MS, Cooke DL, Wang C, Alexander MD. Spatially resolved transcriptomics for evaluation of intracranial vessels in a rabbit model: Proof of concept. Interv Neuroradiol. 2023 Jun;29(3):307-314. doi: 10.1177/15910199221088691. Epub 2022 Mar 21. PMID: 35306920; PMCID: PMC10369109.


dataset_id: STDS0000301
species: Columba livia
organ_parts: crop
cell_types: crop epithelium
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA590607
pmid: 37289658
title:
  Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon

summary:
  Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.

contributors:
  Yujie Wang, Xun Wang, Yi Luo, Jiaman Zhang, Yu Lin, Jie Wu, Bo Zeng, Lei Liu, Peiqi Yan, Jiyuan Liang, Hongrui Guo, Long Jin, Qianzi Tang, Keren Long, Mingzhou Li

citation:
  Wang Y, Wang X, Luo Y, Zhang J, Lin Y, Wu J, Zeng B, Liu L, Yan P, Liang J, Guo H, Jin L, Tang Q, Long K, Li M. Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet. 2023 Jun 8;19(6):e1010746. doi: 10.1371/journal.pgen.1010746. PMID: 37289658; PMCID: PMC10249823.


dataset_id: STDS0000302
title: Transcriptomic profiling of the bovine endosalpinx and endometrium to identify putative embryokines
species: Bos taurus
cell_types: endosalpinx cells, endometrial cells
accessions: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230154
pmid: 37720990
organ_parts:
  bovine endosalpinx, ampulla of the oviduct, endometrium, upper and middle uterine horn, uterine body

summary:
  The objectives of the present study were to characterize the expression of genes encoding for cell signaling ligands in the bovine endosalpinx and endometrium and analyze spatial changes in gene expression. RNA sequencing was performed for the endosalpinx from the ampulla of the oviduct and endometrium from the upper and middle uterine horn and uterine body at day 2 after ovulation from ipsilateral and contralateral sides relative to the ovulatory ovary. Of the 17,827 unique mRNA transcripts mapped, 2,072 were affected by cranial-caudal position in the reproductive tract and 818 were affected by side (false discovery rate < 0.05). There were 334 genes encoding for cell signaling ligands, with 128 genes having greater than two transcripts per million on average. A total of 81 cell signaling ligand genes were affected by position and 24 were affected by side. A data set of the transcriptome of two to four cell embryos was used to identify cell signaling ligand genes that were highly expressed in the ampulla for which there was high expression of the receptor in the embryo. The most expressed ligand-receptor pairs were PSAP/SORT1, MIF/CXCR4, GPI/AMFR, and KITLG/KIT. These cell signaling ligands, as well as others whose gene is expressed in the endosalpinx and endometrium, may influence early embryonic development. Spatial changes throughout the reproductive tract highlight the distinctive expression profile of the oviduct versus the endometrium, including a set of the identified genes encoding for cell signaling ligands, and highlight the local influence of the ovary. The results also show the continuity of expression for large numbers of genes in the reproductive tract.NEW & NOTEWORTHY Examination of the transcriptome of the endosalpinx and endometrium revealed the degree to which gene expression in the reproductive tract varies spatially. The expression of genes encoding cell signaling molecules that could potentially regulate embryonic development was also identified.

contributors:
  Quinn A Hoorn, Maria Belen Rabaglino, Tatiane S Maia, Masroor Sagheer, Dailin Fuego, Zongliang Jiang, Peter J Hansen

citation:
  Hoorn QA, Rabaglino MB, Maia TS, Sagheer M, Fuego D, Jiang Z, Hansen PJ. Transcriptomic profiling of the bovine endosalpinx and endometrium to identify putative embryokines. Physiol Genomics. 2023 Nov 1;55(11):557-564. doi: 10.1152/physiolgenomics.00064.2023. Epub 2023 Sep 18. PMID: 37720990.


dataset_id: STDS0000303
species: Brugia malayi, Wolbachia
organ_parts: reproductive tissue, developing embryos
accessions: https://doi.org/10.17632/8f62vydg3z.1
pmid: 37838705
title:
  Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale

summary:
  Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.

contributors:
  Hailey Sounart, Denis Voronin, Yuvarani Masarapu, Matthew Chung, Sami Saarenpää, Elodie Ghedin, Stefania Giacomello

citation:
  Sounart H, Voronin D, Masarapu Y, Chung M, Saarenpää S, Ghedin E, Giacomello S. Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale. Nat Commun. 2023 Oct 14;14(1):6500. doi: 10.1038/s41467-023-42237-y. PMID: 37838705; PMCID: PMC10576761.


dataset_id: STDS0000304
title: Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus
species: Macaca spp.
organ_parts: infundibular (INF), paraventricular nuclei (PVN)
cell_types: microglia
accessions: https://db.cngb.org/search/project/CNP0003785
pmid: 38325338
summary:
  The hypothalamus plays a crucial role in the progression of obesity and diabetes; however, its structural complexity and cellular heterogeneity impede targeted treatments. Here, we profiled the single-cell and spatial transcriptome of the hypothalamus in obese and sporadic type 2 diabetic macaques, revealing primate-specific distributions of clusters and genes as well as spatial region, cell-type-, and gene-feature-specific changes. The infundibular (INF) and paraventricular nuclei (PVN) are most susceptible to metabolic disruption, with the PVN being more sensitive to diabetes. In the INF, obesity results in reduced synaptic plasticity and energy sensing capability, whereas diabetes involves molecular reprogramming associated with impaired tanycytic barriers, activated microglia, and neuronal inflammatory response. In the PVN, cellular metabolism and neural activity are suppressed in diabetic macaques. Spatial transcriptomic data reveal microglia's preference for the parenchyma over the third ventricle in diabetes. Our findings provide a comprehensive view of molecular changes associated with obesity and diabetes.

contributors:
  Ying Lei, Xian Liang, Yunong Sun, Ting Yao, Hongyu Gong, Zhenhua Chen, Yuanqing Gao, Hui Wang, Ru Wang, Yunqi Huang, Tao Yang, Miao Yu, Longqi Liu, Chun-Xia Yi, Qing-Feng Wu, Xingxing Kong, Xun Xu, Shiping Liu, Zhi Zhang, Tiemin Liu

citation:
  Lei Y, Liang X, Sun Y, Yao T, Gong H, Chen Z, Gao Y, Wang H, Wang R, Huang Y, Yang T, Yu M, Liu L, Yi CX, Wu QF, Kong X, Xu X, Liu S, Zhang Z, Liu T. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. Cell Metab. 2024 Feb 6;36(2):438-453.e6. doi: 10.1016/j.cmet.2024.01.003. PMID: 38325338.


dataset_id: STDS0000305
species: Mulberry silkworms
organ_parts: silk glands
cell_types: ecdysone receptor (ultraspiracle) expressing SG cells
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1056443
pmid: 38996068
title:
  The architecture of silk-secreting organs during the final larval stage of silkworms revealed by single-nucleus and spatial transcriptomics

summary:
  Natural silks are renewable proteins with impressive mechanical properties and biocompatibility that are useful in various fields. However, the cellular and spatial organization of silk-secreting organs remains unclear. Here, we combined single-nucleus and spatially resolved transcriptomics to systematically map the cellular and spatial composition of the silk glands (SGs) of mulberry silkworms late in larval development. This approach allowed us to profile SG cell types and cell state dynamics and identify regulatory networks and cell-cell communication related to efficient silk protein synthesis; key markers were validated via transgenic approaches. Notably, we demonstrated the indispensable role of the ecdysone receptor (ultraspiracle) in regulating endoreplication in SG cells. Our atlas presents the results of spatiotemporal analysis of silk-secreting organ architecture late in larval development; this atlas provides a valuable reference for elucidating the mechanism of efficient silk protein synthesis and developing sustainable products made from natural silk.

contributors:
  Yan Ma, Qingjun Li, Yiyun Tang, Zhiyong Zhang, Rongpeng Liu, Qin Luo, Yuting Wang, Jie Hu, Yuqin Chen, Zhiwei Li, Chen Zhao, Yiting Ran, Yuanyuan Mu, Yinghao Li, Xiaoqing Xu, Yuyan Gong, Zihan He, Yongbing Ba, Kaiqi Guo, Keshu Dong, Xiao Li, Wei Tan, Yumeng Zhu, Zhonghuai Xiang, Hanfu Xu

citation:
  Ma Y, Li Q, Tang Y, Zhang Z, Liu R, Luo Q, Wang Y, Hu J, Chen Y, Li Z, Zhao C, Ran Y, Mu Y, Li Y, Xu X, Gong Y, He Z, Ba Y, Guo K, Dong K, Li X, Tan W, Zhu Y, Xiang Z, Xu H. The architecture of silk-secreting organs during the final larval stage of silkworms revealed by single-nucleus and spatial transcriptomics. Cell Rep. 2024 Jul 23;43(7):114460. doi: 10.1016/j.celrep.2024.114460. Epub 2024 Jul 10. PMID: 38996068.


dataset_id: STDS0000306
species: Spiders
organ_parts: secretory epithelium, gland
cell_types: six cell types
accessions: https://www.ebi.ac.uk/ena/browser/view/PRJEB74310
pmid: 39141739
title:
  Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics

summary:
  Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.

contributors:
  Sumalata Sonavane, Sameer Hassan, Urmimala Chatterjee, Lucile Soler, Lena Holm, Annelie Mollbrink, Gabriele Greco, Noah Fereydouni, Olga Vinnere Pettersson, Ignas Bunikis, Allison Churcher, Henrik Lantz, Jan Johansson, Johan Reimegård, Anna Rising

citation:
  Sonavane S, Hassan S, Chatterjee U, Soler L, Holm L, Mollbrink A, Greco G, Fereydouni N, Vinnere Pettersson O, Bunikis I, Churcher A, Lantz H, Johansson J, Reimegård J, Rising A. Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics. Sci Adv. 2024 Aug 16;10(33):eadn0597. doi: 10.1126/sciadv.adn0597. Epub 2024 Aug 14. PMID: 39141739; PMCID: PMC11323941.


dataset_id: STDS0000307
species: Fasciola hepatica
organ_parts: liver fluke Fasciola hepatica
contributors: Svenja Gramberg, Oliver Puckelwaldt, Tobias Schmitt, Zhigang Lu, Simone Haeberlein
accessions: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1047549
pmid: 39414795
title:
  Spatial transcriptomics of a parasitic flatworm provides a molecular map of drug targets and drug resistance genes

summary:
  The spatial organization of gene expression dictates tissue functions in multicellular parasites. Here, we present the spatial transcriptome of a parasitic flatworm, the common liver fluke Fasciola hepatica. We identify gene expression profiles and marker genes for eight distinct tissues and validate the latter by in situ hybridization. To demonstrate the power of our spatial atlas, we focus on genes with substantial medical importance, including vaccine candidates (Ly6 proteins) and drug resistance genes (glutathione S-transferases, ABC transporters). Several of these genes exhibit unique expression patterns, indicating tissue-specific biological functions. Notably, the prioritization of tegumental protein kinases identifies a PKCβ, for which small-molecule targeting causes parasite death. Our comprehensive gene expression map provides unprecedented molecular insights into the organ systems of this complex parasitic organism, serving as a valuable tool for both basic and applied research.

citation:
  Gramberg S, Puckelwaldt O, Schmitt T, Lu Z, Haeberlein S. Spatial transcriptomics of a parasitic flatworm provides a molecular map of drug targets and drug resistance genes. Nat Commun. 2024 Oct 16;15(1):8918. doi: 10.1038/s41467-024-53215-3. PMID: 39414795; PMCID: PMC11484910.


dataset_id: STDS0000308
title: High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae
species: Drosophila melanogaster
organ_parts: midguts, testis
cell_types: larval midgut cells, larval testis cells
accessions: https://db.cngb.org/stomics/flysta3d/
pmid: 35512700
summary:
  Drosophila has long been a successful model organism in multiple biomedical fields. Spatial gene expression patterns are critical for the understanding of complex pathways and interactions, whereas temporal gene expression changes are vital for studying highly dynamic physiological activities. Systematic studies in Drosophila are still impeded by the lack of spatiotemporal transcriptomic information. Here, utilizing spatial enhanced resolution omics-sequencing (Stereo-seq), we dissected the spatiotemporal transcriptomic changes of developing Drosophila with high resolution and sensitivity. We demonstrated that Stereo-seq data can be used for the 3D reconstruction of the spatial transcriptomes of Drosophila embryos and larvae. With these 3D models, we identified functional subregions in embryonic and larval midguts, uncovered spatial cell state dynamics of larval testis, and revealed known and potential regulons of transcription factors within their topographic background. Our data provide the Drosophila research community with useful resources of organism-wide spatiotemporally resolved transcriptomic information across developmental stages.

contributors:
  Mingyue Wang, Qinan Hu, Tianhang Lv, Yuhang Wang, Qing Lan, Rong Xiang, Zhencheng Tu, Yanrong Wei, Kai Han, Chang Shi, Junfu Guo, Chao Liu, Tao Yang, Wensi Du, Yanru An, Mengnan Cheng, Jiangshan Xu, Haorong Lu, Wangsheng Li, Shaofang Zhang, Ao Chen, Wei Chen, Yuxiang Li, Xiaoshan Wang, Xun Xu, Yuhui Hu, Longqi Liu

citation:
  Wang M, Hu Q, Lv T, Wang Y, Lan Q, Xiang R, Tu Z, Wei Y, Han K, Shi C, Guo J, Liu C, Yang T, Du W, An Y, Cheng M, Xu J, Lu H, Li W, Zhang S, Chen A, Chen W, Li Y, Wang X, Xu X, Hu Y, Liu L. High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae. Dev Cell. 2022 May 23;57(10):1271-1283.e4. doi: 10.1016/j.devcel.2022.04.006. Epub 2022 May 4. PMID: 35512700.


