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Type I interferon responsive microglia shape cortical development and behaviorHuman breast cell atlasInflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primatesSEA-AD: Seattle Alzheimer’s Disease Brain Cell AtlasMolecular and spatial signatures of mouse brain aging at single-cell resolutionLungMAP — The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung.Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cellsA single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculatureDNA Methylation Atlas of the Mouse Brain at Single-Cell ResolutionType I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19Insulin is expressed by enteroendocrine cells during human fetal developmentA single-cell transcriptomic atlas spanning the adult rhesus macaque brainSingle-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestryHuman skeletal muscle ageing atlasHigh-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancerA marmoset brain cell census reveals influence of developmental origin and functional class on neuronal identityComparative transcriptomics reveals human-specific cortical featuresSingle cell RNA sequencing of follicular lymphomaA single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cellsA molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencingCellular development and evolution of the mammalian cerebellumHTAN MSK - Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancerEvolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouseHuman cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neuronsThe cellular landscape of breast cancer associated malignant pleural effusionsProfiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomicsMulti-omic profiling of the developing human cerebral cortex at the single cell levelMSK SPECTRUM – Ovarian cancer mutational processes drive site-specific immune evasionSingle cell atlas of CD19 CAR T-cellsScaleBio Single Cell RNA Sequencing of Human PBMCsPediatric FGID lamina propria of ileum biopsies.Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetesAcute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGHA (Balanced) Bone Marrow Reference Map of Hematopoietic DevelopmentSingle-cell atlas of peripheral immune response to SARS-CoV-2 infectionAzimuth meta-analysis of human scRNA-seq datasetsCellular and transcriptional diversity over the course of human lactationSingle-cell transcriptomics characterization of oligodendrocytes and microglia in white matter agingA Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host ResponsesHTAN MSK - Transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategiesAn Atlas of Gene Regulatory Elements in Adult Mouse CerebrumSingle-cell mapping of lymphatic endothelial cells in lymph nodesTranscriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell ResolutionMassively multiplex chemical transcriptomics at single-cell resolutionTranscriptomic cytoarchitecture reveals principles of human neocortex organizationHuman developing neocortex by areaCOVID-19 mRNA vaccine elicits a potent adaptive immune response in the absence of persistent inflammation observed in SARS-CoV-2 infectionSingle-Cell DNA Methylation and 3D Genome Human Brain AtlasA transcriptional cross species map of pancreatic islet cellsSpatial multiomics map of trophoblast development in early pregnancyPhenotypic variation of transcriptomic cell types in mouse motor cortexDysregulation of brain and choroid plexus cell types in severe COVID-19Single cell atlas of the human retinaA spatially resolved atlas of the human lung characterizes a gland-associated immune nicheSingle cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactionsHuman photoreceptor cells from different macular subregions have distinct transcriptional profilesA transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell typesSingle-soma transcriptomics of tangle-bearing neurons in Alzheimer’s diseaseSingle Cell Atlas of Mouse Healthy GingivaLongitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19An Integrated Single Cell Atlas of Human PeriodontitisiPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cellsA single-cell and spatially resolved atlas of human breast cancersSingle-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific featuresA Cellular Anatomy of the Normal Adult Human Prostate and Prostatic UrethraTabula Muris SenisProtracted Neuronal Recruitment in the Temporal Lobe of Young ChildrenUnified comprehensive single-cell atlas of the mouse retinaTabula SapiensSingle-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamicsHuman CellCards Multi-Study CellRef 1.0 AtlasSingle nucleus and spatial transcriptomic profiling of human healthy hamstring tendonLive Human Microglia Single-cell RNA-seqCells of the adult human heartThyroid hormone remodels cortex to coordinate body-wide metabolism and explorationSpatial and cell type transcriptional landscape of human cerebellar developmentSingle-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responsesBlood and immune development in human fetal bone marrow and Down syndromeCell Types of the Human Retina and Its Organoids at Single-Cell ResolutionSingle cell derived mRNA signals across human kidney tumorsCell atlas of the human ocular anterior segment: Tissue-specific and shared cell typesscRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservationEarly human lung immune cell development and its role in epithelial cell fateSingle-cell transcriptomics of human T cells reveals tissue and activation signatures in health and diseaseSingle-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell statesSingle-cell gene expression profiling of SARS-CoV-2 infected human cell linesMuraro PancreasSingle-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease ActivitySingle-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal MetaplasiaMultiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetesSingle-cell analysis of prenatal and postnatal human cortical developmentSingle cell RNA sequencing of bone marrow mononuclear cells from healthy donors and B-cell lymphoma patients following CD19 CAR T-cell therapyIntra- and Inter-cellular Rewiring of the Human Colon during Ulcerative ColitisIdentification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastomaSingle Cell Multiome Atlas of the Human Fetal RetinaAbdominal White Adipose TissueSingle-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal HeterogeneityImmunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s diseaseImmune microniches shape intestinal Treg functionCell-type specific analysis of physiological action of estrogen inmouse oviductsAn integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell typesConstruction of a human cell landscape at single-cell levelCellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencingMouse perinatal heart maturation scRNA-seqDevelopmental cell programs are co-opted in inflammatory skin diseasePersistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patientsImpaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19Asian Immune Diversity Atlas (AIDA)A blood atlas of COVID-19 defines hallmarks of disease severity and specificityA human cell atlas of fetal gene expressionHarmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastomaCells of the human intestinal tract mapped across space and timeSpatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage nichesA Cellular atlas of the human fallopian tube reveals the metamorphosis of secretory epithelial cells during the menstrual cycle and menopauseSingle cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsResolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humansMultimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progressionSingle-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degenerationA single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pupSingle-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy responseA cell atlas of human thymic development defines T cell repertoire formationA molecular cell atlas of COVID-19 initiation in human lungSingle-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s DiseaseMapping the developing human immune system across organsSingle-cell RNA-seq reveals the cell-type-specific molecular and genetic associations to lupusMulti-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinomaA taxonomy of transcriptomic cell types across the isocortex and hippocampal formationDevelopmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbationSpatially resolved multiomics of human cardiac nichesSingle-cell transcriptome analysis reveals differential nutrient absorption functions in human intestineHuman Brain Cell Atlas v1.0Humoral immunity at the brain borders in homeostasisSpatiotemporal analysis of human intestinal development at single-cell resolutionAdult mouse cortical cell taxonomy revealed by single cell transcriptomicsCell atlas of antigen-presenting and stromal cells from the human intestineGeneration of complex human induced pluripotent stem cell-derived bone marrow organoidsHTAN-CHOP - Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A-rearranged leukemiaIntegrated adult and foetal heart single-cell RNA sequencingSingle cell RNA sequencing of paw skin from healthy and Col7a1 knockout (RDEB) miceA single-cell transcriptome atlas of the adult human retinaPathogenic variants damage cell composition and single cell transcription in cardiomyopathiesSampling peripheral blood and matched nasal swabs from donors with prior immunodeficiencies and autoimmune conditions infected with SARS-CoV-2A human embryonic limb cell atlas resolved in space and timeSingle cell RNA sequencing of CD19 CAR T-cell infusion productsHealthy living donor kidneyAn alternative cell cycle coordinates multiciliated cell differentiationSingle-cell roadmap of human gonadal developmentA proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomicsSingle-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsSARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cellsHypoMap – a unified single cell gene expression atlas of the murine hypothalamusSingle-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cellsA molecular single-cell lung atlas of lethal COVID-19Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitroA molecular cell atlas of the human lung from single cell RNA sequencingIntegration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular DegenerationSingle-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesHuman Trophoblast OrganoidsA comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discoveryHuman and mouse dermal fibroblast atlasAn atlas of healthy and injured cell states and niches in the human kidneyTime-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19Cortical brain samples from C9-ALS, C9-ALS/FTD, C9-FTD patients and age matched controlsSingle-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastomaHTAN VUMC - Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polypsIntratumoral heterogeneity in recurrent pediatric pilocytic astrocytomasSingle-cell eQTL mapping identifies cell type specific genetic control of autoimmune diseaseStress-induced RNA–chromatin interactions promote endothelial dysfunctionLungMAP — Human data from a broad age healthy donor groupSingle cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidneyHuman γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the lifespanCell Atlas of The Human Fovea and Peripheral RetinaA Coding and Non-Coding Atlas of the Human Arterial CellMapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seqHigh-Resolution Transcriptomic Landscape of the Human Submandibular GlandIschemia Reperfusion Responses in Human Lung Transplants at the Single Cell ResolutionSpatiotemporal immune zonation of the human kidneyIntegrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature ThymocytesSex-Specific Control of Human Heart Maturation by the Progesterone ReceptorCITEseq of JDM PBMCsMolecular and cellular evolution of the primate dorsolateral prefrontal cortexComparative Analysis of Commercial Single-Cell RNA Sequencing TechnologiesCross-dementia human brain snRNA-seq (Rexach et al 2024)Single-nucleus cross-tissue molecular reference maps to decipher disease gene functionSingle-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF TherapyHigh-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathyUrethral luminal epithelia are castration-insensitive cells of the proximal prostateHCA kidney seed network: University of MichiganSpatial multi-omic map of human myocardial infarctionEpithelial zonation along the mammalian small intestine defines five discrete metabolic domainsBrain matters: Unveiling the Distinct Contributions of Region, Age, and Sex to Glia diversity and CNS FunctionA spatially resolved single cell genomic atlas of the adult human breastSingle-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liverSingle-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacyDistinct microbial and immune niches of the human coloniPain atlasSingle-cell transcriptomic atlas for adult human retinaEarly role for a Na+,K+-ATPase (ATP1A3) in brain developmentIntegrated analysis of multimodal single-cell dataAcute response to pathogens in the early human placenta at single-cell resolutionTranscriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programsSingle-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degenerationSingle-cell genomics improves the discovery of risk variants and genes of atrial fibrillationSingle-cell multi-omics analysis of the immune response in COVID-19Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast primingSingle-cell reconstruction of the early maternal–fetal interface in humansThe integrated Human Lung Cell AtlasMolecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomicsSingle-cell reconstruction of follicular remodeling in the human adult ovaryNeuron type-specific effects of human aging and sex on DNA methylation and transcriptionSingle nuclei RNA- sequencing from the white matter of individuals with progressive MS and non-neurological controlsThe landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colonSingle cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaIntegrative single-cell multi-omics of CD19-CARpos and CARneg T cells suggest drivers of immunotherapy response in B-ALLEmphysema Cell AtlasCOVID-19 immune features revealed by a large-scale single-cell transcriptome atlasA human breast atlas integrating single-cell proteomics and transcriptomicsDirect Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair ResponseA human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fatesLocal and systemic responses to SARS-CoV-2 infection in children and adultsCross-tissue immune cell analysis reveals tissue-specific features in humansMolecular and cellular dynamics of the developing human neocortex at single-cell resolutionHVS: Human variation studyCharting human development using a multi-endodermal organ atlas and organoid modelsCellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seqDifferential cell composition and split epidermal differentiation in human palm, sole, and hip skinMolecular characterization of selectively vulnerable neurons in Alzheimer's DiseaseMapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancerA single-cell atlas of human and mouse white adipose tissueHigh Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and PathwaysMultiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway ActivationAn atlas of healthy and injured cell states and niches in the human kidney (Version 1.5)Spatially mapping T cell receptors and transcriptomesSingle-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation PatternsA single-cell atlas of the aging mouse ovaryDissecting novel myeloid-derived cell states through single-cell RNA-Seq and its impact on clinical outcome across tumor typesSpatial transcriptomic maps of whole mouse embryos reveal principles of neural tube patterningA molecularly defined and spatially resolved cell atlas of the whole mouse brainShared and distinct transcriptomic cell types across neocortical areas