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Plaque AtlasSingle-cell reconstruction of follicular remodeling in the human adult ovaryMolecular characterization of selectively vulnerable neurons in Alzheimer's DiseaseSpatially mapping T cell receptors and transcriptomesComprehensive cell atlas of the first-trimester developing human brainShared and distinct transcriptomic cell types across neocortical areasscRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservationSingle-cell transcriptomics of human T cells reveals tissue and activation signatures in health and diseaseA human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fatesHTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironmentAbdominal White Adipose TissueSingle-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot StudySingle-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell statesSingle-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal HeterogeneitySingle-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease ActivityMuraro PancreasSingle-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal MetaplasiaSingle-cell transcriptomics reveals gene expression dynamics of human fetal kidney developmentSingle-cell analysis of prenatal and postnatal human cortical developmentSingle-cell genomics improves the discovery of risk variants and genes of atrial fibrillationSingle-cell gene expression profiling of SARS-CoV-2 infected human cell linesMultiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetesCOVID-19 immune features revealed by a large-scale single-cell transcriptome atlasAn atlas of healthy and injured cell states and niches in the human kidneyStress-induced RNA–chromatin interactions promote endothelial dysfunctionIntegrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature ThymocytesSingle 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 ColitisHuman γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the lifespanSingle cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidneySingle Cell Multiome Atlas of the Human Fetal RetinaSingle cell atlas of CD19 CAR T-cellsNeuron type-specific effects of human aging and sex on DNA methylation and transcriptionCellular and transcriptional diversity over the course of human lactationIdentification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastomaSingle-cell transcriptomics characterization of oligodendrocytes and microglia in white matter agingA molecular cell atlas of COVID-19 initiation in human lungAn 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 profilingMapping the developing human immune system across organsThe integrated Human Lung Cell AtlasSampling peripheral blood and matched nasal swabs from donors with prior immunodeficiencies and autoimmune conditions infected with SARS-CoV-2Differential cell composition and split epidermal differentiation in human palm, sole, and hip skinSpatial 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-19LungMAP — 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 sequencingA Cellular atlas of the human fallopian tube reveals the metamorphosis of secretory epithelial cells during the menstrual cycle and menopauseiPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cellsCell Atlas of The Human Fovea and Peripheral RetinaAdult mouse cortical cell taxonomy revealed by single cell transcriptomicsA 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 leukemiaSingle-cell transcriptomes from human kidneys reveal the cellular identity of renal tumorsMapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seqA molecular single-cell lung atlas of lethal COVID-19Human Trophoblast OrganoidsA comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discoveryHuman and mouse dermal fibroblast atlasAcute response to pathogens in the early human placenta at single-cell resolutionAn integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell typesSingle-cell multi-omics analysis of the immune response in COVID-19High-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathyCell-type specific analysis of physiological action of estrogen inmouse oviductsSingle-cell reconstruction of the early maternal–fetal interface in humansHigh-Resolution Transcriptomic Landscape of the Human Submandibular GlandIntegrative single-cell multi-omics of CD19-CARpos and CARneg T cells suggest drivers of immunotherapy response in B-ALLCellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencingCross-dementia human brain snRNA-seq (Rexach et al 2024)Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast primingConstruction of a human cell landscape at single-cell levelMouse perinatal heart maturation scRNA-seqDevelopmental cell programs are co-opted in inflammatory skin diseaseA human embryonic limb cell atlas resolved in space and timePersistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patientsCITEseq of JDM PBMCsMolecular and cellular evolution of the primate dorsolateral prefrontal cortexiPain atlasAsian Immune Diversity Atlas (AIDA)Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19Comparative Analysis of Commercial Single-Cell RNA Sequencing TechnologiesA blood atlas of COVID-19 defines hallmarks of disease severity and specificityHTAN MSK - Transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategiesInflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primatesA single-cell atlas of the aging mouse ovaryHCA kidney seed network: University of MichiganSingle cell atlas of the human retinaHuman breast cell atlasDistinct microbial and immune niches of the human colonMolecular and spatial signatures of mouse brain aging at single-cell resolutionEarly role for a Na+,K+-ATPase (ATP1A3) in brain developmentSingle cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cellsCells of the human intestinal tract mapped across space and timeType I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage nichesDNA Methylation Atlas of the Mouse Brain at Single-Cell ResolutionA cell atlas of human thymic development defines T cell repertoire formationA human cell atlas of fetal gene expressionSingle cell and spatial transcriptomics in Sjögren’s Disease-affected Human Salivary GlandsIntegrated analysis of multimodal single-cell dataSingle-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestryA taxonomy of transcriptomic cell types across the isocortex and hippocampal formationInsulin is expressed by enteroendocrine cells during human fetal developmentScaleBio Single Cell RNA Sequencing of Human PBMCsA single-cell transcriptomic atlas spanning the adult rhesus macaque brainCell 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 fateHuman skeletal muscle ageing atlasType I interferon responsive microglia shape cortical development and behaviorHigh-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancerIntratumoral heterogeneity in recurrent pediatric pilocytic astrocytomasSingle cell RNA sequencing of follicular lymphomaA single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cellsMolecular and cellular dynamics of the developing human neocortex at single-cell resolutionMulti-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinomaLungMAP — The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung.Single-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 cerebellumThe cellular landscape of breast cancer associated malignant pleural effusionsHuman cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neuronsSingle-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programsResolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humansSingle-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s diseaseHigh Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and PathwaysHuman Brain Cell Atlas v1.0Pathogenic variants damage cell composition and single cell transcription in cardiomyopathiesMSK SPECTRUM – Ovarian cancer mutational processes drive site-specific immune evasionMapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancerCross-tissue immune cell analysis reveals tissue-specific features in humansA Coding and Non-Coding Atlas of the Human Arterial CellSingle-nucleus cross-tissue molecular reference maps to decipher disease gene functionPediatric FGID lamina propria of ileum biopsies.A spatially resolved single cell genomic atlas of the adult human breastMouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetesSingle-cell atlas of peripheral immune response to SARS-CoV-2 infectionA (Balanced) Bone Marrow Reference Map of Hematopoietic DevelopmentSingle cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myelomaCharting human development using a multi-endodermal organ atlas and organoid modelsA Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host ResponsesLocal and systemic responses to SARS-CoV-2 infection in children and adultsAn Atlas of Gene Regulatory Elements in Adult Mouse CerebrumCellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seqCell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epitheliumComparative transcriptomics reveals human-specific cortical featuresSingle-cell and spatial mapping Identify cell types and signaling Networks in the human ureterSingle-cell mapping of lymphatic endothelial cells in lymph nodesTranscriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell ResolutionDevelopmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbationA molecularly defined and spatially resolved cell atlas of the whole mouse brainHTAN MSK - Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancerHuman developing neocortex by areaEvolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouseA single-cell transcriptome atlas of the adult human retinaProfiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomicsTranscriptomic cytoarchitecture reveals principles of human neocortex organizationMulti-omic profiling of the developing human cerebral cortex at the single cell levelCOVID-19 mRNA vaccine elicits a potent adaptive immune response in the absence of persistent inflammation observed in SARS-CoV-2 infectionDissecting novel myeloid-derived cell states through single-cell RNA-Seq and its impact on clinical outcome across tumor typesA transcriptional cross species map of pancreatic islet cellsMultimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progressionSingle-Cell DNA Methylation and 3D Genome Human Brain AtlasPhenotypic variation of transcriptomic cell types in mouse motor cortexA marmoset brain cell census reveals influence of developmental origin and functional class on neuronal identitySpatial multiomics map of trophoblast development in early pregnancyLongitudinal 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 SenisA 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 interactionsAcute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGHA Cellular Anatomy of the Normal Adult Human Prostate and Prostatic UrethraMapping the temporal and spatial dynamics of the human endometrium in vivo and in vitroAzimuth meta-analysis of human scRNA-seq datasetsHuman 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 GingivaAn Integrated Single Cell Atlas of Human PeriodontitisMassively multiplex chemical transcriptomics at single-cell resolutionSingle-cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human-specific featuresA single-cell and spatially resolved atlas of human breast cancersProtracted Neuronal Recruitment in the Temporal Lobe of Young ChildrenUnified comprehensive single-cell atlas of the mouse retinaTabula SapiensHuman CellCards Multi-Study CellRef 1.0 AtlasSingle-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 tendonCells of the adult human heartThyroid hormone remodels cortex to coordinate body-wide metabolism and explorationSingle-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responsesSpatial and cell type transcriptional landscape of human cerebellar developmentHarmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastomaCell Types of the Human Retina and Its Organoids at Single-Cell ResolutionSingle cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsA single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pupHumoral immunity at the brain borders in homeostasisSingle-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s DiseaseSingle-cell transcriptome analysis reveals differential nutrient absorption functions in human intestineSpatially resolved multiomics of human cardiac nichesSpatiotemporal analysis of human intestinal development at single-cell resolutionSpatial multi-omic map of human myocardial infarctionMultimodal single-cell sequencing of the human cortex reveals neuronal vulnerability and activated glial cell states in focal cortical dysplasiaGeneration of complex human induced pluripotent stem cell-derived bone marrow organoidsCell atlas of antigen-presenting and stromal cells from the human intestineSingle-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liverIntegrated adult and foetal heart single-cell RNA sequencingSingle-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacySingle-cell roadmap of human gonadal developmentSingle cell RNA sequencing of CD19 CAR T-cell infusion productsAn alternative cell cycle coordinates multiciliated cell differentiationMultiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway ActivationHypoMap – a unified single cell gene expression atlas of the murine hypothalamusA 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 DegenerationSingle-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesSex-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 programsSingle 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 colonEmphysema 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 PatternsBlood and immune development in human fetal bone marrow and Down syndromeSingle cell derived mRNA signals across human kidney tumorsSingle-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degenerationSingle-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 ResolutionSingle-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF TherapyEpithelial 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 Function