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2,063 results for “single cell transcriptomics”
Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
<p>We leveraged single-cell RNA sequencing to understand the early molecular events that define the hepatocyte response to acetaminophen exposure at a subpopulation level. We spatially assigned hepatocytes along the portol-central vein axis by using established landmark genes. By spatially assigning the hepatocytes were were able to account for innate differences in gene expression that existed along this gradient. The excel files herein provide the full list of differentially expressed genes between key subpopulations of interest. Additionally, we classified genes as either pericentral zonated, periportal zonated, or non-zonated, the full list of genes and their spatial assignments are included in the appropriate excel file. </p>
Single-nucleus Transcriptomics of IDH1- and TP53-mutant Glioma Stem Cells Displays Diversified Commitment on Highly Invasive Cancer Progenitors
<p><strong>Fig. S1</strong>. <strong>Marker genes for Seurat clusters.</strong> (<strong>A</strong>) distribution of marker genes for cluster 0 on the 2D-UMAP space. (<strong>B</strong>) distribution of marker genes for cluster 1 on the 2D-UMAP space. (<strong>C</strong>) distribution of marker genes for cluster 2 on the 2D-UMAP space. (<strong>D</strong>) distribution of marker genes for cluster 3 on the 2D-UMAP space. (<strong>E</strong>) distribution of marker genes for cluster 4 on the 2D-UMAP space. (<strong>F</strong>) distribution of marker genes for cluster 5 on the 2D-UMAP space. (<strong>G</strong>) Stuck violin plot of marker gene expression for Seurat clusters (bottom panel) and their annotation (right side panel). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S2</strong>. <strong>Expression of genes marking cell malignization.</strong> (<strong>A</strong>) expression of collagens in Surat clusters (bottom panel) (<strong>B</strong>) expression of genes linked to Migration and ECM in Surat clusters (bottom panel) (<strong>C</strong>) expression of genes classified as Proto-oncogenes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S3</strong>. <strong>Expression of genes involved in proliferation and survival of cancer cells.</strong> (<strong>A</strong>) Genes involved in Wnt-pathway in Surat clusters (bottom panel). (<strong>B</strong>) Genes involved in Akt-pathway in Surat clusters (bottom panel). (<strong>C</strong>) Genes inducing resistance to cancer therapeutics in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.\</p> <p><strong>Fig. S4</strong>. <strong>Expression of genes marking CSC profile.</strong> (<strong>A</strong>) Ion channel genes in Surat clusters (bottom panel). (<strong>B</strong>) Antioncogenes in Surat clusters (bottom panel). <strong>C</strong>. Stem-cell genes in Surat clusters (bottom panel). (<strong>D</strong>) Antiapoptotic genes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S5</strong>. <strong>Genes differentially expressed between UMAP clusters</strong>. (<strong>A</strong>) Heatmap for wt-GSCs. (<strong>B</strong>) Heatmap for mt-GSCs. Upper colour panel in the heatmap designates Seurat clusters. Gene expression is indicated by continuous colour panel starting from the most downregulated (blue) to the most upregulated (red).</p> <p><strong>Fig. S6</strong>. <strong>Marker genes defying cell annotations</strong>. (<strong>A</strong>) Stack violin plot displays marker gene expression in wt-GSC clusters. (<strong>B</strong>) Stack violin plot displays marker gene expression in mt-GSC clusters. Genes grouped by cell annotations (side description) and UMAP clusters (down column bar). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S7</strong>. <strong>Differentially expressed proliferation and adhesion pathways comparing mutant samples to wild type.</strong> (<strong>A</strong>) ERBB signalling pathway. (<strong>B</strong>) Wnt signalling pathway. (<strong>C</strong>) Genes linked to Focal adhesion. (<strong>D</strong>) Genes classified as Cell adhesion molecules. Red rectangles display upregulated genes (proteins), green rectangles define downregulated genes (proteins). Pictures obtained by KEGG pathview.</p> <p><strong>Table S1. Glioma genotyping primers</strong></p> <p><strong>Table S2. Smart-seq2 Primers</strong></p>
Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation
<p>Raw microscopy images underlying the publication "Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation"</p>
Single-cell and spatial transcriptomics of cardiac neural crest reveal a dual role of vinculin in Tgf beta signaling and cell-extracellular matrix interaction during cardiac outflow tract development
<p>single-cell RNA-seq data analysis:</p> <p>all.cncc.combined.EMBO.mapped.Rdata: public CNCC single-cell RNA-seq data integration</p> <p>E13.5_CNCC_merged_updated.Rdata: single-cell RNA-seq data of E13.5 CNCC generated in Elly lab</p> <p>all.seurat.GFP.Rdata: scRNA-seq data with GFP detected</p> <p>visium.merge_AB.control.Rdata: R processed ST data for slice A and B</p> <p>visium.merge_CD.mutant.Rdata: R processed ST data for slice A and B</p> <p> </p>
Datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis
<p>20 benchmark scRNA-seq datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis. In every datasets .zip files, it provided raw data files, the processed R code and the corresponding R objects. The datasets.xlsx file provided the detailed information of 20 datasets.</p>
Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients
<p>This dataset contains the processed scRNA-seq data and code used to investigate the association between lung cancers and COVID-19. Please refer to the article 'Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients' for the detailed data and method description.</p> <p>covid_cancer.rds: the processed scRNA-seq data saved as a Seurat object.</p> <p>notebooks.zip: Jupyter notebooks containing code for data analysis.</p>
Immune Signature of Chronic Hand Eczema Unveiled by Spatial Transcriptomics and Single-Cell Proteomics
ClinicalTrials.gov study NCT06884163. IPD Sharing: NO. Countries: 1. Publications: 6.
Molecular Taxonomy of Surgically-harvested Ocular Tissues Defined by Single-cell Transcriptomics
ClinicalTrials.gov study NCT04682054. IPD Sharing: YES. Countries: 1. Publications: 4.
Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes
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The transcriptomic landscape of normal and ineffective erythropoiesis at single cell resolution
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Single cell transcriptomics of of Abedinium reveals a new early-branching dinoflagellate lineage
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Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
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Single cell transcriptomic analyses reveal the impact of bHLH factors on human retinal organoid development
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Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ
<p>Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed 10X based single cell sequencing on both normal and DBZ treated organoids, and on endometrial and ovarian tumours.</p>
Integrative analyses of single-cell transcriptome and immune profiling reveal clonal expansion of T cells in the blood and cerebrospinal fluid of Parkinson's disease
<p>An increasing number of studies has indicated that the immune system plays important roles in the pathogenesis of Parkinson's disease. However, little is known about the contribution of adaptive immune responses in Parkinson's disease. Here, we performed comprehensive integrative analyses of single-cell transcriptome and immune profiling of the blood of 8 Parkinson's patients and 13 healthy controls as well as the cerebrospinal fluid of 6 Parkinson's patients, 4 Alzheimer's patients, 5 mild cognitive impairment (MCI) patients and 9 healthy controls. In total, 22 T cell subsets with distinct functions and clonalities were identified from 121,402 T cells. We observed significant clonal expansion of effector CD8+ T cells in Parkinson's patients, which formed a gradient of transcriptional states from central memory CD8+ T cells to early effector CD8+ T cells followed by terminal effector CD8+ T cells. Shared TCRs in this progression suggest TCRs may be involved in the state transition of CD8+ T cells stimulated by antigens. Notably, we also found that a group of clonally expanded cytotoxic CD4+ T cells were significantly increased in Parkinson's patients compared to controls, suggesting their cytotoxic roles in Parkinson's disease. Finally, we screened putative TCR-antigen pairs that existed in both blood and cerebrospinal fluid of patients with Parkinson's disease. These results reveal an adaptive immune response in the blood and cerebrospinal fluid of Parkinson's disease and provide novel evidence of clonal, antigen-experienced T cells patrolling in the blood and cerebrospinal fluid of Parkinson's disease.</p>
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
<p>Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid <em>Olkasia</em> as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by <em>Ploeotia</em> spp.), <em>Lentomonas</em>, and <em>Keelungia</em> form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes <em>Rapaza</em>, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (<em>Anisonema</em> and <em>Dinema</em> spp.), '<em>Heteronema</em> II' (represented by <em>H. vittatum</em>), and a clade of <em>Neometanema</em> plus Aphagea. Among 'peranemid' phagotrophs, <em>Chasmostoma</em> branches with included <em>Urceolus</em>, and <em>Peranema</em> with the undescribed '<em>Jenningsia</em> II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that <em>Entosiphon</em> is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.</p>
Single cell RNA-seq transcriptomic profile of circulating immune and progenitor cells in a mouse model of neonatal hypoxic/ischemic (HI) brain damage.
<p>Hematopoietic cells play a pivotal role in regulating the inflammatory and reparative immune responses triggered after ischemic tissue damage. The response initiated within the injured tissue leads to compositional and transcriptional changes in circulating hematopoietic and progenitor cells, which have been utilized as biomarkers. While the importance of different immune and progenitor cell subtypes in the development of ischemic damage has been extensively researched in adult tissue injuries, there has been limited investigation in neonates. This is a critical developmental stage where ischemic damage can result in severe and irreversible health consequences if not promptly treated. To determine how ischemic damage could affect circulating cells in neonates, we have induced hypoxic-ischemic (HI) brain damage in seven-day-old mice, characterized by focal white and gray-matter injury (Rice-Vannucci model). Brain damage and circulating cells were analyzed at 48h post-HI, the intermediate reparative/inflammatory response phase post-injury. We applied scRNAseq to dissect the transcriptional and cellular composition changes in the peripheral blood of HI-treated and SHAM control neonates. This study provides the first scRNAseq dataset for immune and progenitor circulating cells in newborns with cerebral HI damage. It may help to identify biomarkers and selective therapeutic approaches aimed at modulating inflammatory and reparative pathways. </p><p>CD1 postnatal day 7 (P7) mice were subjected to hypoxic/ischemic (HI) brain injury by permanent ligation of the left common carotid artery followed, after 2h recover, by relocation to a hypoxia chamber for 90 minutes. Sham control mice (SHAM) underwent a skin incision and wound closure followed by hypoxia exposure. Circulating blood cells were collected from SHAM and HI mice at P9. After red blood cells (RBC) lysis, 7AAD-Ter119- cells were FACS sorted and analysed using sc RNAseq. Other samples were FACS sorted for CD45+CD11+ and CD45-CD31+ cells and mixed.</p>
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
<p>This dataset contains gene expression values, i. e. transcript counts, of 278 intestinal epithelial cells.</p>
Cellular and molecular heterogeneities and signatures, and pathological trajectories of fatal COVID-19 lungs defined by spatial single-cell transcriptome analysis
<p>Spatial in-situ data analysis.</p>
Single-Cell and Spatial Transcriptomics Analysis of Steatotic Donor Liver Susceptibility to Post-Transplant Injury
ClinicalTrials.gov study NCT07362745. IPD Sharing: NO. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.