CELLxGENE logoCollectionsDatasetsGene Expression
Help & Documentation



Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF TherapyA molecular single-cell lung atlas of lethal COVID-19Single-cell atlas of peripheral immune response to SARS-CoV-2 infectionHumoral immunity at the brain borders in homeostasisMSK SPECTRUM – Ovarian cancer mutational processes drive site-specific immune evasionAn atlas of healthy and injured cell states and niches in the human kidneySingle cell derived mRNA signals across human kidney tumorsAn Atlas of Gene Regulatory Elements in Adult Mouse CerebrumMolecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomicsA transcriptional cross species map of pancreatic islet cellsA proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomicsAn integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell typesEmphysema Cell AtlasMultimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progressionShared and distinct transcriptomic cell types across neocortical areasCell Atlas of The Human Fovea and Peripheral RetinaSingle-nucleus cross-tissue molecular reference maps to decipher disease gene functionA human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fatesSingle-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responsesThe integrated Human Lung Cell AtlasSingle-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsPathogenic variants damage cell composition and single cell transcription in cardiomyopathiesA human cell atlas of fetal gene expressionAcute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGHCell atlas of the human ocular anterior segment: Tissue-specific and shared cell typesEvolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouseSingle-cell multi-omics analysis of the immune response in COVID-19Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cellsA Cellular Anatomy of the Normal Adult Human Prostate and Prostatic UrethraAdult mouse cortical cell taxonomy revealed by single cell transcriptomicsSingle cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactionsMapping the developing human immune system across organsDevelopmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbationDirect Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair ResponseA single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculatureSpatiotemporal immune zonation of the human kidneyInflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primatesSingle-soma transcriptomics of tangle-bearing neurons in Alzheimer’s diseaseLive Human Microglia Single-cell RNA-seqBlood and immune development in human fetal bone marrow and Down syndromeIntegrated adult and foetal heart single-cell RNA sequencingA comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discoveryA single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cellsHypoMap – a unified single cell gene expression atlas of the murine hypothalamusHigh-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancerUrethral luminal epithelia are castration-insensitive cells of the proximal prostateSingle-cell transcriptomics characterization of oligodendrocytes and microglia in white matter agingHuman developing neocortex by areaSingle-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal HeterogeneityA molecular cell atlas of the human lung from single cell RNA sequencingImmunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastomaSingle-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degenerationA single-cell transcriptome atlas of the adult human retinaIntegrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature ThymocytesSingle-cell gene expression profiling of SARS-CoV-2 infected human cell linesHCA kidney seed network: University of MichiganSingle-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cellsSingle-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degenerationSingle-cell transcriptomes of the human skin reveal age-related loss of fibroblast primingSingle-cell transcriptomics of human T cells reveals tissue and activation signatures in health and diseaseSingle-cell RNA-seq reveals the cell-type-specific molecular and genetic associations to lupusSingle-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation PatternsLungMAP — Human data from a broad age healthy donor groupTabula Muris SenisImpaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19Stress-induced RNA–chromatin interactions promote endothelial dysfunctionSingle-cell reconstruction of follicular remodeling in the human adult ovaryDNA Methylation Atlas of the Mouse Brain at Single-Cell ResolutionMolecular characterization of selectively vulnerable neurons in Alzheimer's DiseaseSingle cell RNA sequencing of follicular lymphomaLongitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19Early role for a Na+,K+-ATPase (ATP1A3) in brain developmentMassively multiplex chemical transcriptomics at single-cell resolutionMuraro PancreasLungMAP — The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung.Spatiotemporal analysis of human intestinal development at single-cell resolutionSingle cell RNA sequencing of CD19 CAR T-cell infusion productsSpatial multi-omic map of human myocardial infarctionPhenotypic variation of transcriptomic cell types in mouse motor cortexSingle-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell statesA transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell typesIntegration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular DegenerationCellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seqSEA-AD: Seattle Alzheimer’s Disease Brain Cell AtlasHigh Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and PathwaysCells of the adult human heartAsian Immune Diversity Atlas (AIDA)scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservationCross-tissue immune cell analysis reveals tissue-specific features in humansSingle-cell reconstruction of the early maternal–fetal interface in humansIntra- and Inter-cellular Rewiring of the Human Colon during Ulcerative ColitisSingle-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamicsIntegrated analysis of multimodal single-cell dataCell Types of the Human Retina and Its Organoids at Single-Cell ResolutionMultiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetesThe landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colonSingle cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsSampling peripheral blood and matched nasal swabs from donors with prior immunodeficiencies and autoimmune conditions infected with SARS-CoV-2Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesSingle-cell eQTL mapping identifies cell type specific genetic control of autoimmune diseaseHarmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastomaIdentification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastomaLocal and systemic responses to SARS-CoV-2 infection in children and adultsMouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetesA blood atlas of COVID-19 defines hallmarks of disease severity and specificitySingle-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s DiseaseDistinct microbial and immune niches of the human colonHuman cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neuronsSingle-cell transcriptome analysis reveals differential nutrient absorption functions in human intestineSingle-cell transcriptomic atlas for adult human retinaA cell atlas of human thymic development defines T cell repertoire formationTranscriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell ResolutionCells of the human intestinal tract mapped across space and timeA Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host ResponsesSingle-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal MetaplasiaAzimuth meta-analysis of human scRNA-seq datasetsSingle cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidneyIntratumoral heterogeneity in recurrent pediatric pilocytic astrocytomasCharting human development using a multi-endodermal organ atlas and organoid modelsMapping the temporal and spatial dynamics of the human endometrium in vivo and in vitroSingle-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy responseSingle-cell roadmap of human gonadal developmentAbdominal White Adipose TissueSingle cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaA molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencingHTAN MSK - Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancerA taxonomy of transcriptomic cell types across the isocortex and hippocampal formationHTAN VUMC - Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polypsMolecular and spatial signatures of mouse brain aging at single-cell resolutionSpatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage nichesHuman breast cell atlasHTAN MSK - Transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategiesTime-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19Insulin is expressed by enteroendocrine cells during human fetal developmentTabula SapiensConstruction of a human cell landscape at single-cell levelCOVID-19 immune features revealed by a large-scale single-cell transcriptome atlasSingle cell RNA sequencing of bone marrow mononuclear cells from healthy donors and B-cell lymphoma patients following CD19 CAR T-cell therapyDifferential cell composition and split epidermal differentiation in human palm, sole, and hip skinTranscriptomic diversity of cell types across the adult human brainA spatially resolved single cell genomic atlas of the adult human breast