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Early role for a Na+,K+-ATPase (ATP1A3) in brain developmentMolecular and cellular dynamics of the developing human neocortex at single-cell resolutionIntra- and Inter-cellular Rewiring of the Human Colon during Ulcerative ColitisSingle Cell Multiome Atlas of the Human Fetal RetinaSingle cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cellsThe landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colonTranscriptomic Analysis of Air-Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial DifferentiationType I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19Cells of the adult human heartSingle-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestrySpatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage nichesMultimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasiaA cell atlas of human thymic development defines T cell repertoire formationDissecting novel myeloid-derived cell states through single-cell RNA-Seq and its impact on clinical outcome across tumor typesDNA Methylation Atlas of the Mouse Brain at Single-Cell ResolutionA human cell atlas of fetal gene expressionA single-cell transcriptomic atlas spanning the adult rhesus macaque brainSingle cell and spatial transcriptomics in Sjögren’s Disease-affected Human Salivary GlandsIntegrated analysis of multimodal single-cell dataBronchopulmonary DysplasiaSingle-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesA taxonomy of transcriptomic cell types across the isocortex and hippocampal formationHTAN CHOP - Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiringInsulin is expressed by enteroendocrine cells during human fetal developmentScaleBio Single Cell RNA Sequencing of Human PBMCsCell atlas of the human ocular anterior segment: Tissue-specific and shared cell typesSingle-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degenerationEarly human lung immune cell development and its role in epithelial cell fateSingle-nucleus transcriptomic analysis of human dorsal root ganglion neurons.Type I interferon responsive microglia shape cortical development and behaviorAsian Immune Diversity Atlas (AIDA)Intratumoral heterogeneity in recurrent pediatric pilocytic astrocytomasHuman skeletal muscle ageing atlasSingle cell RNA sequencing of follicular lymphomaA single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cellsHigh-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancerHuman γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the lifespanLungMAP — The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung.Pediatric FGID lamina propria of ileum biopsies.Charting human development using a multi-endodermal organ atlas and organoid modelsTranscriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell ResolutionSingle-cell RNA-seq reveals the cell-type-specific molecular and genetic associations to lupusSEA-AD: Seattle Alzheimer’s Disease Brain Cell AtlasA single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculatureCellular development and evolution of the mammalian cerebellumMouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetesSingle-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitmentSmoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airwaysDevelopmental Regulation of Endothelial-to-Hematopoietic Transition from iPSCsSingle-cell and spatial mapping Identify cell types and signaling Networks in the human ureterHuman circulating hematopoietic stem and progenitor cells in aging, cytopenia and MDSSingle-cell reconstruction of follicular remodeling in the human adult ovaryThe cellular landscape of breast cancer associated malignant pleural effusionsCOVID-19 mRNA vaccine elicits a potent adaptive immune response in the absence of persistent inflammation observed in SARS-CoV-2 infectionComprehensive cell atlas of the first-trimester developing human brainHuman cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neuronsSingle-cell transcriptomics of human T cells reveals tissue and activation signatures in health and diseaseSingle-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programsExploring the Utility of snRNA-seq in Profiling Human Bladder Tissue: A Comprehensive Comparison with scRNA-seqAbdominal White Adipose TissueSpatial multiomics map of trophoblast development in early pregnancyResolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humansHypoMap – a unified single cell gene expression atlas of the murine hypothalamusSingle-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s diseaseIntegrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patientsHigh Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and PathwaysSingle-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal HeterogeneityHuman Brain Cell Atlas v1.0Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomicsCharacterisation of human papillomavirus (HPV)-positive (immune hot) and HPV-negative (immune cold) head and neck tumors by single cell RNA sequencingPathogenic variants damage cell composition and single cell transcription in cardiomyopathiesAn integrated transcriptomic cell atlas of human neural organoidsMulti-omic profiling of the developing human cerebral cortex at the single cell levelA pancreatic islet scRNA-seq atlas from 48 non-diabetic, prediabetic and type 2 diabetic individuals of matched demographic and ethnic backgroundsSingle-cell analysis of prenatal and postnatal human cortical developmentMapping the temporal and spatial dynamics of the human endometrium in vivo and in vitroHuman photoreceptor cells from different macular subregions have distinct transcriptional profilesAzimuth meta-analysis of human scRNA-seq datasetsAn Integrated Single Cell Atlas of Human PeriodontitisSingle-cell genomics improves the discovery of risk variants and genes of atrial fibrillationPlaque AtlasHuman Oral and Craniofacial Cell AtlasSingle-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific featuresStress-induced RNA–chromatin interactions promote endothelial dysfunctionAn integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell typesSingle cell RNA sequencing of bone marrow mononuclear cells from healthy donors and B-cell lymphoma patients following CD19 CAR T-cell therapyCOVID-19 immune features revealed by a large-scale single-cell transcriptome atlasMapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancerTranscriptional profiling of murine oligodendrocyte precursor cells across the lifespanSingle cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidneyA Coding and Non-Coding Atlas of the Human Arterial CellNeuron type-specific effects of human aging and sex on DNA methylation and transcriptionSingle cell atlas of CD19 CAR T-cellsSingle-nucleus cross-tissue molecular reference maps to decipher disease gene functionIdentification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastomaSingle-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot StudyDifferential cell composition and split epidermal differentiation in human palm, sole, and hip skinA spatially resolved single cell genomic atlas of the adult human breastSpatial transcriptomic maps of whole mouse embryos reveal principles of neural tube patterningImmunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19Single-cell atlas of peripheral immune response to SARS-CoV-2 infectionStromal cell diversity associated with immune evasion in human triple‐negative breast cancerUnified comprehensive single-cell atlas of the mouse retinaSingle cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaHuman CellCards Multi-Study CellRef 1.0 AtlasiPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cellsSingle-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamicsLive Human Microglia Single-cell RNA-seqSingle nucleus and spatial transcriptomic profiling of human healthy hamstring tendonThyroid hormone remodels cortex to coordinate body-wide metabolism and explorationThe integrated Human Lung Cell AtlasSpatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer SubtypesSingle-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsHuman Trophoblast OrganoidsHigh-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathyHarmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastomaHigh-Resolution Transcriptomic Landscape of the Human Submandibular GlandA human embryonic limb cell atlas resolved in space and timeCellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seqHuman subcutaneous and visceral adipocyte atlases uncover classical and non-classical adipocytes and depot-specific patternsIntegrative single-cell multi-omics of CD19-CARpos and CARneg T cells suggest drivers of immunotherapy response in B-ALLSimultaneous profiling of transcription and chromatin accessibility at the single-cell level for postnatal human brain developmentHuman and mouse dermal fibroblast atlasAcute response to pathogens in the early human placenta at single-cell resolutionSingle-cell transcriptomes of the human skin reveal age-related loss of fibroblast primingSingle-cell multi-omics analysis of the immune response in COVID-19Construction of a human cell landscape at single-cell levelDevelopmental cell programs are co-opted in inflammatory skin diseaseMouse perinatal heart maturation scRNA-seqCross-dementia human brain snRNA-seq (Rexach et al 2024)Single-cell mapping of lymphatic endothelial cells in lymph nodesHTAN MSK - Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancerGeneration of complex human induced pluripotent stem cell-derived bone marrow organoidsDevelopmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbationTranscriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart diseaseA molecularly defined and spatially resolved cell atlas of the whole mouse brainHuman developing neocortex by areaRecruited macrophages elicit atrial fibrillationMolecular characterization of selectively vulnerable neurons in Alzheimer's DiseaseA Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary DiseaseSpatially mapping T cell receptors and transcriptomesEvolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouseAutomatic cell-type harmonization and integration across Human Cell Atlas datasetsA single-cell transcriptome atlas of the adult human retinaSingle-cell census of murine glioblastoma subtypesTranscriptomic cytoarchitecture reveals principles of human neocortex organizationA transcriptional cross species map of pancreatic islet cellsShared and distinct transcriptomic cell types across neocortical areasA Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host ResponsesThe cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccinationSingle-Cell DNA Methylation and 3D Genome Human Brain AtlasPhenotypic variation of transcriptomic cell types in mouse motor cortexA spatial human thymus cell atlas mapped to a continuous tissue axisA marmoset brain cell census reveals influence of developmental origin and functional class on neuronal identityHTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironmentMouse Post-Flu Time SeriesLongitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19Dysregulation of brain and choroid plexus cell types in severe COVID-19Tabula Muris SenisComparative transcriptomics reveals human-specific cortical featuresSingle-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell statesSingle-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease ActivitySingle cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactionsCystic Fibrosis and healthy control biopsyAcute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGHMuraro PancreasA Cellular Anatomy of the Normal Adult Human Prostate and Prostatic UrethraA Balanced Bone Marrow Reference Map of Hematopoietic DevelopmentSingle-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal MetaplasiaSingle-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacySingle cell atlas of the human optic nerveSingle-cell transcriptomics reveals gene expression dynamics of human fetal kidney developmentSingle-soma transcriptomics of tangle-bearing neurons in Alzheimer’s diseaseSingle-cell RNA sequencing of glioblastoma cases with tissue sampled from tumor core to macroscopically normal cortexSingle Cell Atlas of Mouse Healthy GingivaA transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell typesSingle-cell gene expression profiling of SARS-CoV-2 infected human cell linesCell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epitheliumMultiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetesSingle cell atlas of the human trabecular meshwork and ciliary bodySingle cell atlas of the human ocular surfaceMassively multiplex chemical transcriptomics at single-cell resolutionAn atlas of healthy and injured cell states and niches in the human kidneyIntegrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature ThymocytesCells of the human intestinal tract mapped across space and timeSingle cell atlas of the human retinal pigment epithelium and the choroidTranscriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient HeterogeneityAnomalous Epithelial Variations and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary DiseaseExploring cellular changes in ruptured human quadriceps tendons at single-cell resolutionComparative Analysis of Commercial Single-Cell RNA Sequencing TechnologiesCellular and transcriptional diversity over the course of human lactationA cell atlas of the human fallopian tube throughout the menstrual cycle and menopauseSingle-cell transcriptomics characterization of oligodendrocytes and microglia in white matter agingA single-cell and spatially resolved atlas of human breast cancersAn atlas of healthy and injured cell states and niches in the human kidney (Version 1.5)Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profilingProtracted Neuronal Recruitment in the Temporal Lobe of Young ChildrenSampling peripheral blood and matched nasal swabs from donors with prior immunodeficiencies and autoimmune conditions infected with SARS-CoV-2HYPOMAP: A comprehensive spatio-cellularmap of the human hypothalamusA spatially resolved atlas of the human lung characterizes a gland-associated immune nicheSpatiotemporal analysis of human intestinal development at single-cell resolutionSingle cell atlas of the human retinaSingle Nuclei Atlas of Innervated and Denervated Mouse MuscleLungMAP — Human data from a broad age healthy donor groupA molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencingCell Atlas of The Human Fovea and Peripheral RetinaAdult mouse cortical cell taxonomy revealed by single cell transcriptomicsIntegrated human endoderm-derived organoids cell atlas (HEOCA)A molecular cell atlas of the human lung from single cell RNA sequencingImmune microniches shape intestinal Treg functionHTAN-CHOP - Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A-rearranged leukemiaMapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seqA molecular single-cell lung atlas of lethal COVID-19Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responsesMolecular and cellular evolution of the primate dorsolateral prefrontal cortexSpatial and cell type transcriptional landscape of human cerebellar developmentA comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discoverySingle nuclei RNA- sequencing from the white matter of individuals with progressive MS and non-neurological controlsCell-type specific analysis of physiological action of estrogen inmouse oviductsCyclin replacement hijacks the cell cycle's genetic regulatory program to orchestrate multiciliogenesisSingle-cell reconstruction of the early maternal–fetal interface in humansCell Types of the Human Retina and Its Organoids at Single-Cell ResolutionMolecular Signatures of Resilience to Alzheimer’s Disease in Neocortical Layer 4 NeuronsSingle cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsA single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pupMultimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progressionCellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencingPersistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patientsCITEseq of JDM PBMCsSpatial multi-omic map of human myocardial infarctionMSK SPECTRUM – Ovarian cancer mutational processes drive site-specific immune evasionLocal and systemic responses to SARS-CoV-2 infection in children and adultsiPain atlasA human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fatesMultimodal benchmarking dataset for renal cortex characterization (mBDRC)Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liverSingle cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish.Integrated adult and foetal heart single-cell RNA sequencingWild type adult thymusDistinct microbial and immune niches of the human colonImpaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19Cross-tissue immune cell analysis reveals tissue-specific features in humansA blood atlas of COVID-19 defines hallmarks of disease severity and specificityCell atlas of antigen-presenting and stromal cells from the human intestineHTAN MSK - Transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategiesA multi-region single nucleus transcriptomic atlas of Parkinson’s diseaseSingle-cell roadmap of human gonadal developmentInflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primatesSingle cell RNA sequencing of CD19 CAR T-cell infusion productsA single-cell atlas of the aging mouse ovaryAn alternative cell cycle coordinates multiciliated cell differentiationHCA kidney seed network: University of MichiganSpatially resolved multiomics of human cardiac nichesAn Atlas of Gene Regulatory Elements in Adult Mouse CerebrumMultiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway ActivationMulti-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinomaTabula SapiensMapping the developing human immune system across organsHumoral immunity at the brain borders in homeostasisMolecular and spatial signatures of mouse brain aging at single-cell resolutionHuman breast cell atlasscRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservationSingle-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s DiseaseSingle-cell transcriptome analysis reveals differential nutrient absorption functions in human intestineA proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomicsSingle-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cellsSARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cellsIntegration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular DegenerationSex-Specific Control of Human Heart Maturation by the Progesterone ReceptorTime-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19Spatiotemporal immune zonation of the human kidneyHTAN VUMC - Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polypsUrethral luminal epithelia are castration-insensitive cells of the proximal prostateMolecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomicsSingle-cell transcriptomic atlas for adult human retinaTranscriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programsEmphysema Cell 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 ResponseHVS: Human variation studyA single-cell atlas of human and mouse white adipose tissueSingle-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation PatternsSingle cell derived mRNA signals across human kidney tumorsSingle-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy responseSingle cell RNA sequencing of paw skin from healthy and Col7a1 knockout (RDEB) miceHealthy living donor kidneyCortical 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 glioblastomaSingle-cell eQTL mapping identifies cell type specific genetic control of autoimmune diseaseIschemia Reperfusion Responses in Human Lung Transplants at the Single Cell ResolutionBrain matters: Unveiling the Distinct Contributions of Region, Age, and Sex to Glia diversity and CNS FunctionEpithelial zonation along the mammalian small intestine defines five discrete metabolic domainsBlood and immune development in human fetal bone marrow and Down syndromeSingle-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degenerationSingle-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF TherapyA molecular cell atlas of COVID-19 initiation in human lung