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Healthy living donor kidneyIschemia Reperfusion Responses in Human Lung Transplants at the Single Cell ResolutionTranscriptome 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 DiseaseConstruction of a human cell landscape at single-cell levelMapping the developing human immune system across organsMolecular characterization of selectively vulnerable neurons in Alzheimer's DiseaseExploring cellular changes in ruptured human quadriceps tendons at single-cell resolutionA Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host ResponsesComparative Analysis of Commercial Single-Cell RNA Sequencing TechnologiesSingle-Cell DNA Methylation and 3D Genome Human Brain AtlasCellular and transcriptional diversity over the course of human lactationPhenotypic variation of transcriptomic cell types in mouse motor cortexA spatial human thymus cell atlas mapped to a continuous tissue axisHTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironmentThe landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colonMouse Post-Flu Time SeriesSingle-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 transcriptomics characterization of oligodendrocytes and microglia in white matter agingMuraro PancreasSingle-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal MetaplasiaA transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell typesA Cellular Anatomy of the Normal Adult Human Prostate and Prostatic UrethraSingle-cell transcriptomics reveals gene expression dynamics of human fetal kidney developmentSingle-cell RNA sequencing of glioblastoma cases with tissue sampled from tumor core to macroscopically normal cortexAn atlas of healthy and injured cell states and niches in the human kidneyA single-cell and spatially resolved atlas of human breast cancersSingle cell RNA sequencing of the human embryonic meninges at 5-13 weeks post conceptionImmune Response mechanisms in the cerebrospinal fluid in leptomeningeal disease at single cell resolutionDeciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profilingEarly role for a Na+,K+-ATPase (ATP1A3) in brain developmentIntra- and Inter-cellular Rewiring of the Human Colon during Ulcerative ColitisMolecular and cellular dynamics of the developing human neocortex at single-cell resolutionSingle Cell Multiome Atlas of the Human Fetal RetinaHuman subcutaneous and visceral adipocyte atlases uncover classical and non-classical adipocytes and depot-specific patternsSampling peripheral blood and matched nasal swabs from donors with prior immunodeficiencies and autoimmune conditions infected with SARS-CoV-2Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouseCells 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 formationDNA 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 brainLNCS: Atlas of healthy human lymph nodes with and without ex vivo adjuvant stimulationSingle 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 formationCell 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 fateSpatiotemporal analysis of human intestinal development at single-cell resolutionType I interferon responsive microglia shape cortical development and behaviorHYPOMAP: A comprehensive spatio-cellularmap of the human hypothalamusHuman skeletal muscle ageing atlasA spatially resolved atlas of the human lung characterizes a gland-associated immune nicheSingle cell atlas of the human retinaLungMAP — The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung.A Balanced Bone Marrow Reference Map of Hematopoietic DevelopmentA marmoset brain cell census reveals influence of developmental origin and functional class on neuronal identityInflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primatesSEA-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 cerebellumCell Atlas of The Human Fovea and Peripheral RetinaSmoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airwaysImmune microniches shape intestinal Treg functionMapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seqSingle-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responsesSpatial and cell type transcriptional landscape of human cerebellar developmentThe cellular landscape of breast cancer associated malignant pleural effusionsCyclin replacement hijacks the cell cycle's genetic regulatory program to orchestrate multiciliogenesisCell Types of the Human Retina and Its Organoids at Single-Cell ResolutionMolecular Signatures of Resilience to Alzheimer’s Disease in Neocortical Layer 4 NeuronsMultimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progressionPersistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patientsCellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencingCITEseq of JDM PBMCsSpatial multi-omic map of human myocardial infarctionSingle-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 programsComprehensive cell atlas of the first-trimester developing human brainExploring the Utility of snRNA-seq in Profiling Human Bladder Tissue: A Comprehensive Comparison with scRNA-seqA single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pupAbdominal White Adipose TissueSpatial multiomics map of trophoblast development in early pregnancyA human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fatesMultimodal benchmarking dataset for renal cortex characterization (mBDRC)HypoMap – 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 diseaseSingle-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liverHigh Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and PathwaysSingle cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish.Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal HeterogeneityIntegrated adult and foetal heart single-cell RNA sequencingHuman Brain Cell Atlas v1.0Wild type adult thymusProfiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomicsDistinct microbial and immune niches of the human colonPathogenic variants damage cell composition and single cell transcription in cardiomyopathiesImpaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19An integrated transcriptomic cell atlas of human neural organoidsCross-tissue immune cell analysis reveals tissue-specific features in humansMulti-omic profiling of the developing human cerebral cortex at the single cell levelHTAN 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 developmentHuman photoreceptor cells from different macular subregions have distinct transcriptional profilesA single-cell atlas of the aging mouse ovaryAzimuth meta-analysis of human scRNA-seq datasetsAn alternative cell cycle coordinates multiciliated cell differentiationAn Integrated Single Cell Atlas of Human PeriodontitisSingle cell RNA sequencing of CD19 CAR T-cell infusion productsSingle-cell genomics improves the discovery of risk variants and genes of atrial fibrillationHCA kidney seed network: University of MichiganHuman Oral and Craniofacial Cell AtlasSpatially resolved multiomics of human cardiac nichesSingle-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific featuresAn Atlas of Gene Regulatory Elements in Adult Mouse CerebrumStress-induced RNA–chromatin interactions promote endothelial dysfunctionMultiomic 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 carcinomaAn 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 CellHumoral immunity at the brain borders in homeostasisMolecular and spatial signatures of mouse brain aging at single-cell resolutionHuman breast cell atlasSingle-nucleus cross-tissue molecular reference maps to decipher disease gene functionscRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservationIdentification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastomaSingle-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s DiseaseSingle cell atlas of CD19 CAR T-cellsA 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 cellsA spatially resolved single cell genomic atlas of the adult human breastSARS-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 DegenerationSingle-cell atlas of peripheral immune response to SARS-CoV-2 infectionStromal cell diversity associated with immune evasion in human triple‐negative breast cancerTime-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19Spatiotemporal immune zonation of the human kidneySingle cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaHTAN 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 prostateHuman CellCards Multi-Study CellRef 1.0 AtlasMolecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomicsiPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cellsSingle-cell transcriptomic atlas for adult human retinaSingle-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamicsTranscriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programsMultimodal profiling reveals tissue-directed signatures of human immune cells altered with ageEmphysema Cell AtlasA human breast atlas integrating single-cell proteomics and transcriptomicsThyroid hormone remodels cortex to coordinate body-wide metabolism and explorationDirect Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair ResponseThe integrated Human Lung Cell AtlasHVS: Human variation studySpatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer SubtypesA single-cell atlas of human and mouse white adipose tissueSingle-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsHuman Trophoblast OrganoidsSingle-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation PatternsHigh-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathySingle-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy responseHarmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastomaSingle cell RNA sequencing of paw skin from healthy and Col7a1 knockout (RDEB) miceHigh-Resolution Transcriptomic Landscape of the Human Submandibular GlandCortical brain samples from C9-ALS, C9-ALS/FTD, C9-FTD patients and age matched controlsCellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seqSingle-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastomaCharacterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolutionIntegrative 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 developmentBrain 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 domainsAcute response to pathogens in the early human placenta at single-cell resolutionSingle-cell eQTL mapping identifies cell type specific genetic control of autoimmune diseaseSingle cell atlas of large B-cell lymphomaBlood and immune development in human fetal bone marrow and Down syndromeSingle-cell transcriptomes of the human skin reveal age-related loss of fibroblast primingSingle-cell multi-omics analysis of the immune response in COVID-19Single-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 TherapyDevelopmental cell programs are co-opted in inflammatory skin diseaseMouse perinatal heart maturation scRNA-seqCross-dementia human brain snRNA-seq (Rexach et al 2024)A molecular cell atlas of COVID-19 initiation in human lungSingle-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 perturbationDissecting novel myeloid-derived cell states through single-cell RNA-Seq and its impact on clinical outcome across tumor typesInsulin is expressed by enteroendocrine cells during human fetal developmentHuman developing neocortex by areaTranscriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart diseaseRecruited macrophages elicit atrial fibrillationHigh-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancerMSK SPECTRUM – Ovarian cancer mutational processes drive site-specific immune evasionA Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary DiseaseSpatially mapping T cell receptors and transcriptomesHuman and mouse dermal fibroblast atlasAutomatic cell-type harmonization and integration across Human Cell Atlas datasetsA single-cell transcriptome atlas of the adult human retinaSingle-cell census of murine glioblastoma subtypesSingle nucleus transcriptomic atlas of human foetal tendonCOVID-19 mRNA vaccine elicits a potent adaptive immune response in the absence of persistent inflammation observed in SARS-CoV-2 infectionTranscriptomic cytoarchitecture reveals principles of human neocortex organizationShared and distinct transcriptomic cell types across neocortical areasSingle cell atlas of the human retinal pigment epithelium and the choroidA cell atlas of the human fallopian tube throughout the menstrual cycle and menopauseIntegrated human endoderm-derived organoids cell atlas (HEOCA)Human circulating hematopoietic stem and progenitor cells in aging, cytopenia and MDSThe cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccinationAn atlas of healthy and injured cell states and niches in the human kidney (Version 1.5)Protracted Neuronal Recruitment in the Temporal Lobe of Young ChildrenSingle cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cellsTranscriptomic Analysis of Air-Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial DifferentiationDevelopmental Zebrafish Reference AtlasSingle cell atlas of the human ocular surfaceType I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19Single-nucleus transcriptomic analysis of human dorsal root ganglion neurons.Single cell derived mRNA signals across human kidney tumorssnRNA-seq of human kidney with ureteral obstructionPlaque AtlasSingle Nuclei Atlas of Innervated and Denervated Mouse MuscleLungMAP — Human data from a broad age healthy donor groupHTAN CHOP - Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiringScaleBio Single Cell RNA Sequencing of Human PBMCsIntratumoral heterogeneity in recurrent pediatric pilocytic astrocytomasLongitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung diseaseTranscriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell ResolutionCharting human development using a multi-endodermal organ atlas and organoid modelsDysregulation of brain and choroid plexus cell types in severe COVID-19Single cell RNA sequencing of follicular lymphomaA single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cellsTabula Muris SenisHuman γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the lifespanA molecularly defined and spatially resolved cell atlas of the whole mouse brainPediatric FGID lamina propria of ileum biopsies.Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestineA molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencingMulti-omic and spatial analysis of mouse kidneys highlights sex-specific differences in gene regulation across the lifespanSingle-cell RNA-seq reveals the cell-type-specific molecular and genetic associations to lupusSingle cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactionsMouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetesAsian Immune Diversity Atlas (AIDA)Cystic Fibrosis and healthy control biopsyMolecular and cellular evolution of the primate dorsolateral prefrontal cortexSingle-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitmentDevelopmental Regulation of Endothelial-to-Hematopoietic Transition from iPSCsAcute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGHAdult mouse cortical cell taxonomy revealed by single cell transcriptomicsA molecular cell atlas of the human lung from single cell RNA sequencingHTAN-CHOP - Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A-rearranged leukemiaSingle-cell and spatial mapping Identify cell types and signaling Networks in the human ureterA molecular single-cell lung atlas of lethal COVID-19Single 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 oviductsSingle-cell reconstruction of the early maternal–fetal interface in humansSingle cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsSingle-cell reconstruction of follicular remodeling in the human adult ovaryA comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discoveryHuman cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neuronsLocal and systemic responses to SARS-CoV-2 infection in children and adultsSingle-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacyResolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humansiPain atlasCharacterisation of human papillomavirus (HPV)-positive (immune hot) and HPV-negative (immune cold) head and neck tumors by single cell RNA sequencingIntegrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patientsA blood atlas of COVID-19 defines hallmarks of disease severity and specificityUnified comprehensive single-cell atlas of the mouse retinaA pancreatic islet scRNA-seq atlas from 48 non-diabetic, prediabetic and type 2 diabetic individuals of matched demographic and ethnic backgroundsSingle-soma transcriptomics of tangle-bearing neurons in Alzheimer’s diseaseSingle-cell analysis of prenatal and postnatal human cortical developmentMapping the temporal and spatial dynamics of the human endometrium in vivo and in vitroTabula SapiensNeuron type-specific effects of human aging and sex on DNA methylation and transcriptionSingle-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot StudySingle cell atlas of the human optic nerveDifferential cell composition and split epidermal differentiation in human palm, sole, and hip skinSpatial transcriptomic maps of whole mouse embryos reveal principles of neural tube patterningSingle Cell Atlas of Mouse Healthy GingivaImmunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19Sex-Specific Control of Human Heart Maturation by the Progesterone ReceptorLive Human Microglia Single-cell RNA-seqSingle nucleus and spatial transcriptomic profiling of human healthy hamstring tendonSingle-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 diabetesComparative transcriptomics reveals human-specific cortical featuresA human embryonic limb cell atlas resolved in space and timeSingle cell atlas of the human trabecular meshwork and ciliary bodyA transcriptional cross species map of pancreatic islet cellsMassively multiplex chemical transcriptomics at single-cell resolutionIntegrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature ThymocytesCells of the human intestinal tract mapped across space and time