HCA Data Portal

HCA Data Portal Platform Updates

Febraury 24, 2025

New projects (8):

  1. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion
  2. A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast
  3. An integrated single cell and spatial transcriptomic map of human white adipose tissue
  4. Early-life inflammation primes a T helper 2 cell-fibroblast niche in skin
  5. Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis
  6. Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations
  7. Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
  8. The Dynamic Transcriptional Cell Atlas of Testis Development During Human Puberty

Updated Projects (2):

  1. A single-cell transcriptome atlas of human early embryogenesis
  2. Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn’s Disease

January 15, 2025

New Raw Data and Metadata (6)

  1. Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade
  2. Human subcutaneous and visceral adipocyte atlases uncover classical and non-classical adipocytes and depot-specific patterns
  3. Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing
  4. Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution
  5. Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia
  6. Mural cell composition and functional analysis in the healing process of human gingiva from periodontal intrabony defects

Updated Raw Data and Metadata (5)

  1. A single-cell transcriptome atlas of human early embryogenesis
  2. A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation
  3. Organoid single-cell genomic atlas uncovers human-specific features of brain development
  4. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
  5. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

December 01, 2024

New Projects (3)

  1. Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions
  2. Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis
  3. Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy

Updated projects (3):

  1. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
  2. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells.
  3. Asian Immune Diversity Atlas (AIDA): Single-cell analysis of human diversity in circulating immune cells (Japan cells)

October 31, 2024

New Raw Data, Metadata, and Contributor-generated Matrices (5)

  1. A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation
  2. Evolution of neuronal cell classes and types in the vertebrate retina
  3. Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas
  4. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma
  5. Single-cell connectomic analysis of adult mammalian lungs

Updated Raw Data and Metadata

  1. Single-cell RNA sequencing of human kidney
  2. Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis
  3. Myofibroblast transcriptome indicates SFRP2hi fibroblast progenitors in systemic sclerosis skin

September 20, 2024

Release Highlights

  • You can now request access to controlled project data and associated metadata.

Some genomic data available in the HCA portal may be regarded as sensitive/protected data under relevant privacy laws. These data are not available through the open-access tier, and instead can only be accessed via managed-access tier. This tier utilizes the Broad Institute’s Data Use Oversight System (DUOS). To learn more about working with such data, please check out this article on Requesting Access to Controlled Access Data.

New Raw Data, Metadata, and Contributor-generated Matrices (1)

  1. Single-cell analysis of human diversity in circulating immune cells (Japan cells)

September 13, 2024

New Raw Data, Metadata, and Contributor-generated Matrices (4)

  1. Activation of CD8+ T Cells in Chronic Obstructive Pulmonary Disease Lung
  2. An Atlas of Cells in the Human Tonsil
  3. Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry
  4. Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure

August 5, 2024

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (3)

  1. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
  2. Dynamic scRNA-seq of live human pancreatic slices reveals functional endocrine cell neogenesis through an intermediate ducto-acinar stage
  3. Human SARS-CoV-2 challenge resolves local and systemic response dynamics

Updated Raw Data and Metadata (30)

  1. A single-cell atlas of human teeth
  2. Single-Cell Transcriptomics of the Human Endocrine Pancreas
  3. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis
  4. Single-cell multi-omics analysis of the immune response in COVID-19
  5. Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes
  6. Anomalous Epithelial Variations and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
  7. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics
  8. Genetic ancestry effects on the response to viral infection are pervasive but cell type specific
  9. Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity
  10. Local and systemic responses to SARS-CoV-2 infection in children and adults
  11. Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing
  12. Organoid single-cell genomic atlas uncovers human-specific features of brain development
  13. Pathogen-induced tissue-resident memory T H 17 (T RM 17) cells amplify autoimmune kidney disease
  14. Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level
  15. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
  16. Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
  17. Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns
  18. Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes
  19. Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
  20. Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response
  21. Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs
  22. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
  23. Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis
  24. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming
  25. Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure
  26. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function
  27. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
  28. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
  29. The single-cell transcriptomic landscape of early human diabetic nephropathy
  30. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

June 28, 2024

Release Highlights

  • A new project is available from the Oral & Craniofacial Biological Network.

New Raw Data, Metadata, and Contributor-generated Matrices (2)

  1. An Atlas of Cells in the Human Tonsil
  2. Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon

Updated Raw Data and Metadata (3)

  1. Recruited macrophages elicit atrial fibrillation
  2. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease
  3. Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

May 29, 2024

Release Highlights

  • New projects are available from the Oral & Craniofacial and Pancreas Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (5)

  1. High-Resolution Transcriptomic Landscape of the Human Submandibular Gland
  2. Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer
  3. Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes
  4. Single-nucleus RNA sequencing and spatial transcriptomics decode cell type-specific drivers underlying IBM pathogenesis
  5. Spatial transcriptomic profiling of human retinoblastoma

May 9, 2024

Release Highlights

  • New projects are available from the Heart, Oral & Craniofacial, and Skin Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (9)

  1. Anatomically distinct fibroblast subsets determine skin autoimmune patterns
  2. Defining cardiac functional recovery in end-stage heart failure at single-cell resolution
  3. Distinct fibroblast progenitor subpopulation expedites regenerative mucosal healing by immunomodulation
  4. Salivary ZG16B expression loss follows exocrine gland dysfunction related to oral chronic graft-versus-host disease
  5. Single cell and lineage tracing studies reveal the impact of CD34+ cells on myocardial fibrosis during heart failure
  6. Single cell atlas of the human retina
  7. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
  8. Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs
  9. Transcriptomic Mapping of Human Parotid Gland at Single-Cell Resolution

Updated Raw Data and Metadata (3)

  1. A cellular census of human lungs identifies novel cell states in health and in asthma
  2. A human cell atlas of the pressure-induced hypertrophic heart
  3. Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids

April 8, 2024

Release Highlights

  • New projects are available from the Eye, Heart, and Pancreas Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (4)

  1. A transcriptional cross species map of pancreatic islet cells
  2. Cardiac cell type-specific gene regulatory programs and disease risk association
  3. Recruited macrophages elicit atrial fibrillation
  4. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation

Updated Raw Data and Metadata (4)

  1. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
  2. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
  3. Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryonic fibroblasts
  4. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

March 20, 2024

Release Highlights

  • New projects are available from the Eye, Heart, Lung, and Pancreas Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (11)

  1. Cell type-specific and disease-associated eQTL in the human lung
  2. A Single-Cell Transcriptome Atlas of the Human Pancreas
  3. Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles
  4. Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response
  5. A human cell atlas of the pressure-induced hypertrophic heart
  6. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB-CD8+ memory T cells and accumulation of type 2 memory T cells
  7. Integrated multiomic characterization of congenital heart disease
  8. Single Nucleus RNA-sequencing Reveals Altered Intercellular Communication and Dendritic Cell Activation in Nonobstructive Hypertrophic Cardiomyopathy
  9. Single-nucleus RNA sequencing in ischemic cardiomyopathy reveals common transcriptional profile underlying end-stage heart failure
  10. Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids
  11. Generation of human islet cell type-specific identity genesets

Updated Raw Data and Metadata (15)

  1. Spatial multi-omic map of human myocardial infarction
  2. Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)
  3. GM-CSF-producing T helper cells: a distinct subset of T helper cells
  4. Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
  5. Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies
  6. Retinal ganglion cell-specific genetic regulation in primary open angle glaucoma
  7. A single-cell transcriptome atlas of human early embryogenesis
  8. Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2
  9. Spatial multiomics map of trophoblast development in early pregnancy
  10. Single-cell RNA sequencing of normal human kidney
  11. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
  12. Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
  13. Ischaemic sensitivity of human tissue by single cell RNA seq
  14. Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
  15. Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina

January 16, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (15)

  1. A Single-Cell Transcriptome Atlas of the Human Pancreas
  2. Identification of neural oscillations and epileptiform changes in human brain organoids
  3. Multi-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma
  4. Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
  5. Single Cell Multiome Atlas of the Human Fetal Retina
  6. Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma
  7. Single-cell analysis reveals innate lymphoid cell lineage infidelity in atopic dermatitis
  8. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
  9. Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type-specific immune regulation in atopic dermatitis
  10. Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy
  11. Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney
  12. Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
  13. Spatially resolved multiomics of human cardiac niches
  14. The serine proteases dipeptidyl-peptidase 4 and urokinase are key molecules in human and mouse scar formation
  15. Transcriptional and Cellular Diversity of the Human Heart

Updated Raw Data and Metadata (26)

  1. Ischaemic sensitivity of human tissue by single cell RNA seq
  2. A Single-Cell Atlas of the Human Healthy Airways
  3. A cellular census of human lungs identifies novel cell states in health and in asthma
  4. A single-cell transcriptome atlas of the adult human retina
  5. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
  6. Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults
  7. An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies
  8. Cryopreservation and post-thaw characterization of dissociated human islet cells
  9. Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium
  10. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
  11. Identification of a unique subset of tissue-resident memory CD4+ T cells in Crohn’s disease
  12. Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
  13. Pro-inflammatory T helper 17 directly harms oligodendrocytes in neuroinflammation
  14. SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells
  15. Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
  16. Single-Cell Transcriptome and Downstream Analyses of Human Stomach Reveal the Cell Diversity and Developmental Features of Gastric and Metaplastic Mucosae
  17. Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell
  18. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
  19. Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
  20. Single-cell Transcriptome Atlas of the Human Corpus Cavernosum
  21. Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
  22. Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
  23. Spatio-temporal immune zonation of the human kidney
  24. The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
  25. The local and systemic response to SARS-CoV-2 infection in children and adults
  26. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition

December 4, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (8)

  1. A spatially resolved single-cell genomic atlas of the adult human breast
  2. An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies
  3. Classification of human chronic inflammatory skin disease based on single-cell immune profiling
  4. Crosstalk of astrocyte, microglia, and neuronal subtypes correlates to Alzheimer’s disease pathology
  5. Neuronal defects in a human cellular model of 22q11.2 deletion syndrome
  6. Single cell transcriptional zonation of human psoriasis skin identifies an alternative immunoregulatory axis conducted by skin resident cells
  7. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye
  8. αβγδ T cells play a vital role in fetal human skin development and immunity

Updated Raw Data and Metadata (4)

  1. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types
  2. Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
  3. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant
  4. Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment

October 31, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (7)

  1. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation
  2. Dysregulation of brain and choroid plexus cell types in severe COVID-19
  3. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex
  4. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms
  5. Single-Cell Transcriptome and Downstream Analyses of Human Stomach Reveal the Cell Diversity and Developmental Features of Gastric and Metaplastic Mucosae
  6. Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
  7. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease

Updated Raw Data and Metadata (5)

  1. A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra
  2. Joint profiling of chromatin accessibility and gene expression in thousands of single cells
  3. Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
  4. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
  5. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

September 27, 2023

Release Highlights

  • New projects are available from the Brain and Lung Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (8)

  1. A molecular cell atlas of the human lung from single-cell RNA sequencing
  2. Allergic inflammatory memory in human respiratory epithelial progenitor cells
  3. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
  4. Molecular characterization of selectively vulnerable neurons in Alzheimer's disease
  5. Phenotype molding of stromal cells in the lung tumor microenvironment
  6. Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment
  7. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19
  8. The ZIP8/SIRT1 axis regulates alveolar progenitor cell renewal in aging and idiopathic pulmonary fibrosis

Updated Raw Data and Metadata (5)

  1. Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds
  2. The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy
  3. A multi-omic single-cell landscape of human gynecologic malignancies
  4. Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages
  5. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant

August 28, 2023

New Raw Data, Metadata, and Contributor-generated Matrices (5)

  1. Cellular development and evolution of the mammalian cerebellum
  2. Dysregulated lung stroma drives emphysema exacerbation by potentiating resident lymphocytes to suppress an epithelial stem cell reservoir
  3. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
  4. Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes
  5. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state

Updated Raw Data and Metadata (23)

  1. A Cellular Atlas of Pitx2-Dependent Cardiac Development
  2. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure
  3. A human single cell atlas of the substantia nigra reveals novel cell specific pathways associated with the genetic risk of Parkinson’s disease and neuropsychiatric disorders
  4. A single-cell survey of the human first-trimester placenta and decidua
  5. CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function
  6. Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease
  7. Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease
  8. Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing
  9. Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq
  10. Dissecting the protein and transcriptional responses of human immune cells to T cell and monocyte specific activation
  11. GM-CSF-producing T helper cells: a distinct subset of T helper cells
  12. Massively parallel single-cell RNA-seq analysis of 26,677 pancreatic islets cells from both healthy and type II diabetic (T2D) donors
  13. Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)
  14. Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors
  15. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human
  16. Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue
  17. Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
  18. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function
  19. Transcriptomic and clonal characterization of T cells in the human central nervous system
  20. A single-cell reference map of transcriptional states for human blood and tissue T cell activation
  21. A single-cell regulatory map of postnatal lung alveologenesis in humans and mice
  22. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification
  23. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

July 27, 2023

New Raw Data, Metadata, and Contributor-generated Matrices (21)

  1. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes
  2. Single-cell genomics improves the discovery of risk variants and genes of cardiac traits
  3. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis
  4. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis
  5. Village in a dish: a model system for population-scale hiPSC studies
  6. Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy
  7. The immune cell landscape in kidneys of patients with lupus nephritis
  8. Multimodal single cell sequencing of human diabetic kidney disease implicates chromatin accessibility and genetic background in disease progression
  9. Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease
  10. Lung transplantation for patients with severe COVID-19
  11. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas
  12. Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell
  13. Marked regional glial heterogeneity in the human white matter of the central nervous system
  14. Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages
  15. A single cell atlas of the human liver tumor microenvironment
  16. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification
  17. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia
  18. Regenerative lineages and immune-mediated pruning in lung cancer metastasis
  19. Single cell landscape of mesenchymal and endothelial cells in healthy human liver
  20. Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin
  21. Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

Updated Raw Data and Metadata (4)

  1. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types
  2. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
  3. A multi-omics atlas of the human retina at single-cell resolution
  4. AIDA

June 26, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (14)

  1. A multi-omic single-cell landscape of human gynecologic malignancies
  2. A multi-omics atlas of the human retina at single-cell resolution
  3. A single-cell regulatory map of postnatal lung alveologenesis in humans and mice
  4. Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults
  5. Characterization of altered molecular mechanisms in Parkinson's disease through cell type-resolved multiomics analyses
  6. Dynamic changes in human single cell transcriptional signatures during fatal sepsis
  7. Human melanocyte development and melanoma dedifferentiation at single-cell resolution
  8. Immune signatures underlying post-acute COVID-19 lung sequelae
  9. Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  10. Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease
  11. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker
  12. Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord
  13. Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression
  14. The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon

Updated Raw Data and Metadata (2)

  1. A single cell atlas of the human proximal epididymis reveals cell-type specific functions and distinct roles for CFTR
  2. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19

June 13, 2023

Release Highlights

  • New projects are available from the Eye, Gut, and Kidney Biological Networks.

  • Several projects were removed from the Data Portal while metadata is being updated. They will be added to the portal again during an upcoming release.

    • COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets (UUID: 61515820-5bb8-45d0-8d12-f0850222ecf0)

    • Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord (UUID: e6773550-c1a6-4949-8643-1a3154cf2670)

New Raw Data, Metadata, and Contributor-generated Matrices (16)

  1. Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
  2. Cell Atlas of The Human Fovea and Peripheral Retina
  3. Construction of A Human Cell Landscape by Single-cell mRNA-seq
  4. Cross-tissue immune cell analysis reveals tissue-specific features in humans
  5. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
  6. Identification of a unique subset of tissue-resident memory CD4+ T cells in Crohn’s disease
  7. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
  8. Intrarenal Single-Cell Sequencing of Hepatitis B Virus Associated Membranous Nephropathy
  9. Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease
  10. Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis
  11. Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions
  12. Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response
  13. Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
  14. Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity
  15. Single-cell sequencing reveals novel cellular heterogeneity in uterine leiomyomas
  16. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Updated Raw Data and Metadata (4)

  1. Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
  2. Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
  3. A single-cell transcriptomic atlas of the human ciliary body
  4. Integrated analysis of multimodal single-cell data

May 11, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (3)

  1. A Partial Picture of the Single-Cell Transcriptomics of Human IgA Nephropathy
  2. Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways
  3. Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer

Updated Raw Data and Metadata (2)

  1. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
  2. Vento-tormo: Single cell profiling of COVID-19 patients: an international data resource from multiple tissues

March 31, 2023

Release Highlights

  • A full project metadata spreadsheet is now available for several projects in the Data Portal. You can download the spreadsheet from the Metadata page for any project where it is available by selecting the download icon under Metadata. Download Metadata

  • A new managed access project, "Spatially organized multicellular immune hubs in human colorectal cancer", is available in the Data Portal.

  • New projects are available from the Blood, Gut, and Kidney Biological Networks.

New Raw Data, Metadata, and Contributor-generated Matrices (10)

  1. Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts
  2. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant
  3. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses
  4. Single-Cell RNA Sequencing in Multiple Pathologic Types of Renal Cell Carcinoma Revealed Novel Potential Tumor-Specific Markers
  5. Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals
  6. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors
  7. Spatially organized multicellular immune hubs in human colorectal cancer
  8. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19
  9. Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk
  10. Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity

February 24, 2023

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (11)

  1. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
  2. Comprehensive cell atlas of the first-trimester developing human brain
  3. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
  4. Integrated analysis of multimodal single-cell data
  5. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
  6. Single-cell Transcriptome Atlas of Testis Aging
  7. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease
  8. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages
  9. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy
  10. The single cell atlas of human endometrial stromal cells
  11. Vento-tormo: Single cell profiling of COVID-19 patients: an international data resource from multiple tissues

Updated Raw Data and Metadata (3)

  1. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
  2. Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk
  3. Comparison of manual and two types of bioprinted kidney organoids by single cell RNA-seq

December 20, 2022

Release Highlights

Raw Data, Metadata, and Contributor-generated Matrices (10)

  1. A Single-Cell Transcriptome Atlas of Glia Diversity in the Human Hippocampus across the Lifespan and in Alzheimer’s Disease
  2. A single-cell transcriptomic atlas of the human ciliary body
  3. HCA seed network precise tumor-nephrectomy samples
  4. Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing
  5. Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior
  6. Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
  7. Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord
  8. Single-cell dissection of the human brain vasculature
  9. Single-nuclei profiling of aged skeletal muscle
  10. Single-nucleus transcriptomic atlas of spinal cord neuron in human

Updated Raw Data and Metadata (6)

  1. A single cell immune cell atlas of human hematopoietic system
  2. Fate-mapping within human iPSC-derived kidney organoids reveals conserved mammalian nephron progenitor lineage relationships
  3. Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells
  4. RNA-Seq from human innate lymphoid cells (ILCs) transitional populations
  5. Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition
  6. Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

November 28, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (10)

  1. Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types
  2. Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium
  3. SARS-CoV-2 infection of the oral cavity and saliva
  4. Single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas
  5. Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues
  6. Single-Cell Lymphocyte Heterogeneity in Advanced Cutaneous T-cell Lymphoma Skin Tumors
  7. Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment
  8. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma
  9. Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons
  10. The regulatory landscapes of human ovarian ageing

Updated Metadata (3)

  1. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
  2. Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
  3. A single-cell reference map of transcriptional states for human blood and tissue T cell activation

October 19, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (4)

  1. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
  2. Differential dynamics of response at single cell resolution following CAR-T therapy in refractory B-cell lymphoma
  3. Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition
  4. Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

Updated Metadata (2)

  1. Expansion of Fcγ Receptor IIIa-Positive Macrophages, Ficolin 1-Positive Monocyte-Derived Dendritic Cells, and Plasmacytoid Dendritic Cells Associated With Severe Skin Disease in Systemic Sclerosis
  2. A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

September 26, 2022

Release Highlights

  • The Data Portal now hosts over 30 million cells! Thank you to the HCA community and all of the contributors that helped us reach this milestone!

New Raw Data, Metadata, and Contributor-generated Matrices (12)

  1. A Single-Cell Characterization of Human Post-implantation Embryos Cultured In Vitro Delineates Morphogenesis in Primary Syncytialization
  2. A Single-Cell Transcriptomic Atlas of Human Skin Aging
  3. A human breast atlas integrating single-cell proteomics and transcriptomics
  4. Defining Transcriptional Signatures of Human Hair Follicle Cell States
  5. Expansion of Fcγ Receptor IIIa-Positive Macrophages, Ficolin 1-Positive Monocyte-Derived Dendritic Cells, and Plasmacytoid Dendritic Cells Associated With Severe Skin Disease in Systemic Sclerosis
  6. Mapping the developing human immune system across organs
  7. Robust temporal map of human in vitro myelopoiesis using single-cell genomics
  8. Single cell transcriptomics of human epidermis identifies basal stem cell transition states
  9. Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord
  10. Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis
  11. Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
  12. The myogenesis program drives clonal selection and drug resistance in rhabdomyosarcoma

Updated Metadata (5)

  1. Single-cell RNA-Seq reveals a developmental atlas of human prefrontal cortex
  2. Profiling of transcribed cis-regulatory elements in single cells
  3. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
  4. Spatial multi-omic map of human myocardial infarction
  5. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

August 23, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (9)

  1. CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo
  2. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
  3. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
  4. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
  5. Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds
  6. Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas
  7. Single Cell Transcriptomics Reveals Cell Type Specific Diversification in Human Heart Failure
  8. Single-cell Transcriptome Atlas of the Human Corpus Cavernosum
  9. The immune cell atlas of human neuroblastoma

Updated Metadata (39)

  1. A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors
  2. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure
  3. A cellular census of human lungs identifies novel cell states in health and in asthma
  4. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
  5. A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
  6. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
  7. Assessing the relevance of organoids to model inter-individual variation
  8. Blood and immune development in human fetal bone marrow and Down syndrome
  9. Construction of a single-cell transcriptomic atlas of 58,243 liver cells from 4 donors and 4 recipient liver transplasnt patients to investigate early allograft dysfunction (EAD)
  10. Decoding Human Megakaryocyte Development
  11. Developmental cell programs are co-opted in inflammatory skin disease
  12. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
  13. Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
  14. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
  15. Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
  16. Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
  17. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
  18. Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
  19. Molecular Architecture of the Mouse Nervous System
  20. Molecular and functional heterogeneity of IL-10-producing CD4+ T cells
  21. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  22. Profiling of transcribed cis-regulatory elements in single cells
  23. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  24. Sampling time-dependent artifacts in single-cell genomics studies
  25. Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
  26. Single Cell RNAseq of primary pulmonary endothelial cells
  27. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
  28. Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
  29. Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
  30. Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
  31. Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
  32. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
  33. Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
  34. Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder
  35. Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations
  36. Spatial multi-omic map of human myocardial infarction
  37. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
  38. The Human and Mouse Enteric Nervous System at Single-Cell Resolution
  39. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition

July 19, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (6)

  1. Lineage recording in human cerebral organoids
  2. Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity
  3. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus
  4. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
  5. The local and systemic response to SARS-CoV-2 infection in children and adults
  6. Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks

Updated Metadata (4)

  1. A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
  2. Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing
  3. Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue
  4. Spatial multi-omic map of human myocardial infarction

June 29, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (11)

  1. A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
  2. A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
  3. Decoding Human Megakaryocyte Development
  4. Memory-like natural killer cells facilitate effector functions of daratumumab in multiple myeloma
  5. Profiling of transcribed cis-regulatory elements in single cells
  6. Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor
  7. Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies
  8. Single-cell deciphering of human fetal innate lymphoid cell development
  9. Single-cell sequencing unveils the heterogeneity of nonimmune cells in chronic apical periodontitis
  10. The Human and Mouse Enteric Nervous System at Single-Cell Resolution
  11. scRNA-seq experiments on human foreskin fibroblasts, foreskin fibroblasts induced directly to retina pigment epithelium, and induced pluripotent stem cell derived retina pigment epithelium

Updated Metadata (28)

  1. Assessing the relevance of organoids to model inter-individual variation
  2. A single cell atlas of human teeth
  3. Blood and immune development in human fetal bone marrow and Down syndrome
  4. Capturing human trophoblast development with naive pluripotent stem cells in vitro
  5. Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
  6. Extreme heterogeneity of influenza virus infection in single cells
  7. Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
  8. Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
  9. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  10. Single Cell RNA Sequencing of Human Milk-Derived Cells Reveals Sub-Populations of Mammary Epithelial Cells with Molecular Signatures of Progenitor and Mature States: a Novel, Non-invasive Framework for Investigating Human Lactation Physiology
  11. Single Cell RNA-Seq profiling human embryonic kidney cortex cells
  12. Single cell RNA-seq of HeLa CCL2
  13. Single cell RNAseq of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
  14. Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
  15. Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)
  16. Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2
  17. Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
  18. Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
  19. Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
  20. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
  21. Single-cell transcriptomics of normal pancreas, intraductal papillary mucinous neoplasm, and pancreatic adenosquamous carcinoma reveals the heterogeneous progression of pancreatic ductal and stromal cells
  22. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
  23. Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
  24. Spatial multi-omic map of human myocardial infarction
  25. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
  26. Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers
  27. The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
  28. The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles

June 9, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (13)

  1. A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors
  2. A single-cell atlas of breast cancer cell lines to study tumour heterogeneity and drug response
  3. CITE-seq of in vitro control and memory-like human NK cells
  4. Combinatorial transcription factor profiles predict mature and functional human islet α and β cells
  5. RNA-Seq from human innate lymphoid cells (ILCs) transitional populations
  6. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  7. Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
  8. Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease
  9. Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity
  10. Skin single cell universe identifies IL-1B/IL23A co-producing CD14+ type 3 dendritic cells in psoriasis
  11. Spatial multi-omic map of human myocardial infarction
  12. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
  13. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Updated Raw Data, Metadata, Contributor-generated Matrices (4)

  1. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
  2. Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
  3. Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue
  4. Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation

April 20, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (19):

  1. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics
  2. A single-cell transcriptome atlas of human early embryogenesis
  3. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
  4. Cells of the human intestinal tract mapped across space and time
  5. Construction of a single-cell transcriptomic atlas of 58,243 liver cells from 4 donors and 4 recipient liver transplasnt patients to investigate early allograft dysfunction (EAD)
  6. Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
  7. Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci
  8. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
  9. Molecular signatures of inflammatory profile and B-cell function in SFTS patients
  10. Retinal ganglion cell-specific genetic regulation in primary open angle glaucoma
  11. Single cell RNA-seq of HeLa CCL2
  12. Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)
  13. Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2
  14. Single cell transcriptome atlases of the developing mouse and human spinal cord
  15. Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
  16. Single-cell RNA-Seq reveals a developmental atlas of human prefrontal cortex
  17. Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder
  18. Single-nucleus transcriptomic profiles of glial cells in human dorsal root ganglion and spinal cord
  19. Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution - scRNA-Seq

Updated Raw Data, Metadata, Contributor-generated Matrices (10):

  1. Blood and immune development in human fetal bone marrow and Down syndrome
  2. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
  3. A cell atlas of human thymic development defines T cell repertoire formation
  4. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
  5. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
  6. Decoding human fetal liver haematopoiesis
  7. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
  8. Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
  9. Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
  10. Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells

March 30, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (11):

  1. A cellular census of human lungs identifies novel cell states in health and in asthma
  2. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
  3. Conserved cell types with divergent features in human versus mouse cortex
  4. Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
  5. Molecular Architecture of the Mouse Nervous System
  6. Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19-associated AKI
  7. Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection
  8. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
  9. Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation
  10. Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers
  11. Microglia Require CD4 T Cells to Complete the Fetal-to-Adult Transition

Updated Raw Data, Metadata, Contributor-generated Matrices (6):

  1. Assessing the relevance of organoids to model inter-individual variation
  2. Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
  3. Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
  4. Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
  5. The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
  6. The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres

February 14, 2022

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (14):

  1. A multi-omics atlas of the human retina at single-cell resolution
  2. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
  3. Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing
  4. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
  5. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
  6. Pseudo-temporal ordering of individual cells reveals regulators of differentiation
  7. Single cell RNA sequencing of human failing heart
  8. Single cell RNAseq analysis of the developmental trajectory of iPSC-derived tenocytes
  9. Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
  10. Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
  11. Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development
  12. Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration
  13. Spatial and single-cell transcriptional landscape of human cerebellar development
  14. The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors

New HCA Data Portal Analysis (19):

  1. Cryopreservation and post-thaw characterization of dissociated human islet cells
  2. Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq
  3. Melanoma infiltration of stromal and immune cells
  4. Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
  5. Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 diabetic donors
  6. Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)
  7. Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors
  8. Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
  9. Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma
  10. Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury
  11. Single-cell RNA-seq reveals heterogeneity within human pre-cDCs
  12. Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
  13. Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease
  14. Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
  15. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
  16. Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations
  17. Systematic comparative analysis of single cell RNA-sequencing methods
  18. Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq
  19. Transcriptomes of 1,529 individual cells from 88 human preimplantation embryos

December 20, 2021

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (21):

  1. A Single-Cell Atlas of the Human Healthy Airways
  2. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
  3. A single-cell atlas of chromatin accessibility in the human genome
  4. An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine
  5. Blood and immune cell development in human fetal bone marrow and in Down syndrome
  6. CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function
  7. Co-evolution of tumor and immune cells during progression of multiple myeloma
  8. Extreme heterogeneity of influenza virus infection in single cells
  9. Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
  10. Identification of distinct synovial fibroblast subsets associated with pain and progression of knee osteoarthritis using single-cell RNA sequencing
  11. Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
  12. Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics
  13. Modeling Hepatoblastoma: Identification of Distinct Tumor Cell Populations and Key Genetic Mechanisms through Single Cell Sequencing (scRNA-seq)
  14. SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells
  15. Sampling time-dependent artifacts in single-cell genomics studies
  16. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
  17. Single-cell ATAC sequencing reveals the mechanism of human breast cancer metastasis
  18. Single-cell RNA sequencing of human femoral head in vivo
  19. Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease
  20. Single-cell sequencing unveils distinct immune microenvironment in human chronic pancreatitis
  21. Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets

Updated Metadata, Raw Data, Contributor-generated Matrices, or HCA Data Portal Analysis (7):

  1. A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells
  2. AIDA pilot data
  3. Distinct microbial and immune niches of the human colon
  4. Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
  5. Single-cell RNA-seq analysis throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types
  6. Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation trajectory
  7. Stress-induced RNA–chromatin interactions promote endothelial dysfunction

November 11, 2021

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (14)

  1. Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
  2. Cryopreservation and post-thaw characterization of dissociated human islet cells
  3. Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease
  4. Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells
  5. Healthy human kidney cell type single cell RNA-seq data
  6. Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
  7. In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution
  8. Mapping Development of the Human Intestinal Niche at Single-Cell Resolution
  9. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
  10. Pro-inflammatory T helper 17 directly harms oligodendrocytes in neuroinflammation
  11. Single Cell RNAseq of primary pulmonary endothelial cells
  12. Single cell RNAseq of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
  13. Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
  14. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

Updated Metadata, Raw Data, Contributor-generated Matrices, or HCA Data Portal Analysis (2)

  1. AIDA pilot data
  2. Single cell RNA sequencing of multiple myeloma II

October 13, 2021

Release Highlights

New Raw Data, Metadata, and Contributor-generated Matrices (14)

  1. A Single-cell Transcriptomic Atlas of Human Intervertebral Disc
  2. A human cell atlas of fetal gene expression
  3. COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis
  4. Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells
  5. Lifespan charactarization of the nasal mucosa
  6. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  7. Single cell RNA-seq of brain glioblastoma samples
  8. Single cell RNA-sequencing on healthy and IPF lung mesenchymal cells
  9. Single cell atlas of the healthy breast
  10. Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
  11. Single-cell analysis of Crohn's disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
  12. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia
  13. Single-cell atlas of human oral mucosa reveals a stromal-neutrophil axis in tissue immunity regulation
  14. Single-cell transcriptomics of normal pancreas, intraductal papillary mucinous neoplasm, and pancreatic adenosquamous carcinoma reveals the heterogeneous progression of pancreatic ductal and stromal cells

New HCA Data Portal Analysis (2)

  1. Census of Immune Cells
  2. Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus

Updated Metadata, Contributor-generated Matrices, or HCA Data Portal Analysis (20)

  1. A single cell atlas of human teeth
  2. Capturing human trophoblast development with naive pluripotent stem cells in vitro
  3. Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
  4. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Female]
  5. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Male]
  6. Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans
  7. Single Cell RNA Sequencing of Human Milk-Derived Cells Reveals Sub-Populations of Mammary Epithelial Cells with Molecular Signatures of Progenitor and Mature States: a Novel, Non-invasive Framework for Investigating Human Lactation Physiology
  8. Single Cell RNA-Seq profiling human embryonic kidney cortex cells
  9. Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
  10. Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
  11. Single-Cell RNA-Seq Analysis of cells from human urine
  12. Single-cell RNA sequencing of human nasal swab from healthy donors
  13. Single-cell RNA-sequencing reveals the landscape of cervical cancer heterogeneity
  14. Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
  15. Single-cell reconstruction of follicular remodeling in the human adult ovary
  16. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
  17. Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
  18. The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
  19. The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
  20. The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles

September 17, 2021

New Raw Data

The HCA Data Portal has added raw data for the following 14 new projects:

  1. A molecular single-cell lung atlas of lethal COVID-19
  2. Capturing human trophoblast development with naive pluripotent stem cells in vitro
  3. Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues
  4. Fate-mapping within human iPSC-derived kidney organoids reveals conserved mammalian nephron progenitor lineage relationships
  5. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Female]
  6. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Male]
  7. Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk
  8. Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans
  9. Single Cell RNA Sequencing of Human Milk-Derived Cells Reveals Sub-Populations of Mammary Epithelial Cells with Molecular Signatures of Progenitor and Mature States: a Novel, Non-invasive Framework for Investigating Human Lactation Physiology
  10. Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
  11. Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
  12. Single-Cell RNA-Seq Analysis of cells from human urine
  13. Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
  14. The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles

Updated Data

The following 3 projects have updated files:

  1. A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells
  2. Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
  3. Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation trajectory

HCA Data Portal now contains data for 14 million estimated cells

August 25, 2021

New Raw Data

The HCA Data Portal has added raw data for the following 12 new projects:

  1. AIDA pilot data
  2. Comparison of manual and two types of bioprinted kidney organoids by single cell RNA-seq
  3. Developmental cell programs are co-opted in inflammatory skin disease
  4. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
  5. Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
  6. Single-cell RNA sequencing of human nasal swab from healthy donors
  7. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
  8. Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse
  9. Single-cell transcriptomics of East-Asian pancreatic islets cells
  10. The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
  11. The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
  12. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition

New Contributor Data

The following projects have new contributor-generated matrix files:

  1. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
  2. Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming

Browser Updates

Selecting "Normal" Samples

To enable easier discovery of normal tissues, we've modified the Specimen Disease search facet on the Explore page so that the "Normal" option is now at the top of the drop-down.

Selecting Normal Samples

Selecting Files by "Content Description"

The File facet has a new Content Description column to enable searching for files by the type of data they contain.

Selecting Files

New Managed Access and Seed Network projects

July 23, 2021

The HCA Data Portal has added its first managed access project.

Contributor-generated cell-by-gene count matrices and associated non-personally identifiable metadata are now available to the whole HCA community from within the HCA Data Portal.

Additionally, the HCA Data Portal now has the first project data from the HCA Seed Networks, which are further developing the Human Cell Atlas by combining the expertise of experimental scientists, software engineers, and physicians.

Managed Access Projects

  1. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Managed access raw data is available from the Synapse database upon successful completion of a data use certificate. To find supplementary links to the managed access datasets in Synapse, navigate to the project detail page in the Data Portal.

Supplementary Links

HCA Seed Networks Projects

  1. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
  2. Stress-induced RNA–chromatin interactions promote endothelial dysfunction
  3. A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells

Additional New or Updated Projects

Projects with new raw data and/or contributor-generated matrices:

  1. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
  2. Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle
  3. Single-cell reconstruction of follicular remodeling in the human adult ovary
  4. Single Cell RNA-Seq profiling human embryonic kidney cortex cells
  5. Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
  6. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
  7. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
  8. A single cell atlas of human teeth
  9. Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
  10. Single-cell RNA sequencing of normal human kidney
  11. Single-cell RNA-sequencing reveals the landscape of cervical cancer heterogeneity
  12. Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
  13. Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
  14. Molecular and functional heterogeneity of IL-10-producing CD4+ T cells
  15. Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming

Projects with new uniformly processed data:

  1. Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
  2. A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra
  3. The emergent landscape of the mouse gut endoderm at single-cell resolution
  4. Microglia Require CD4 T Cells to Complete the Fetal-to-Adult Transition
  5. High throughput error corrected Nanopore single cell transcriptome sequencing
  6. Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease

Data Portal now contains data for 13.5 million cells

June 16, 2021

  • Raw data and contributor-generated matrices are available for 15 new projects. These single-cell data are derived from:
  • Single-cell and single-nucleus
  • 10x 3' v2 and v3 3' and 10x 5' chemistry, Fluidigm C1, Smart-seq2, and sci-CAR ATAC sequencing technologies
  • Adipose tissue, blood, bone marrow, CSF, heart, kidney, lung, oral cavity, ovary, pancreas, prostate, skeletal muscle, testis, and umbilical vein
  • Disease states including COVID-19 infection, intracranial hypertension, multiple sclerosis, and renal cell carcinoma
  • Developmental stages including fetal, child, adolescent, and adult
  • Standardized data, including aligned BAMs and cell-by-gene count matrices (Loom format), are available for 8 additional projects with data derived from:
  • 10x v2 and v3 3' sequencing technologies
  • Brain (superior parietal cortex, middle temporal gyrus, and temporal cortex), epididymis, immune tissue, cortex of the kidney organoid, lymph nodes, placenta (chorionic villus and decidua), spine, testis, and thymus
  • Disease states including Alzheimer disease and cognitive impairment with or without cerebellar ataxia
  • New Jupyter Notebook tutorials for analyzing standardized HCA Data Portal matrix files are available in an Intro-to-HCA-data-on-Terra workspace on the cloud-based platform Terra.
  • After registering, you can try the step-by-step instructions for importing HCA data and analyzing in common community tools such as Bioconductor, Cumulus, Pegasus, Scanpy, and Seurat.

Raw sequencing data and contributor-generated matrices for 23 new projects available for download

May 10, 2021

  • Data Portal now has data for 12.2 million cells, including new standardized analyses for 13 projects as well as raw sequencing data and contributor-generated matrices for 23 new projects.
  • The standardized data, including aligned BAMs and cell-by-gene count matrices (Loom format), are derived from:
  • Human and mouse
  • Single-cell and single-nucleus
  • 10x V2 and V3 3' chemistry
  • Blood, brain (including substantia nigra, developing hippocampus, cortex, retina), liver, lung, mouth, skeletal muscle, skin, spleen, and developing thymus
  • Disease states including HIV, drug hypersensitivity syndrome, multiple sclerosis, and thoracic aortic aneurysm
  • The 23 new projects and contributor-generated matrices include data derived from:
  • Human and mouse
  • Smart-seq2, 10x V2 and V3 3' chemistry, Drop-seq, and Fluidigm C1 sequencing methods
  • Blood, bone marrow, brain, cord blood, epididymis, fetal gonads, immune organ, kidney organoid, lymph nodes, pancreas, skin, and trachea
  • Disease states including Alzheimer's Disease, multiple sclerosis, autoimmune encephalitis, and type 2 diabetes
  • The Matrix Overview guide has been updated to include additional information on matrix batch correction and normalization.

Raw data for 16 new projects now available

April 12, 2021

Raw sequencing data for 16 new projects are now available in the HCA Data Portal Data Browser. These projects include single-cell data derived from:

  • Human and mouse
  • 10x 3’, 10x 5’, Smart-seq2 technologies
  • Small intestine, aorta, brain, skeletal muscle, blood, pancreas, tonsil, lung, skin, immune system, kidney, and eye
  • Airway basal stem cells exposed to SARS-CoV-2
  • Disease states, including Crohn's Disease, aneurysm, Multiple Sclerosis, HIV, Type 2 Diabetes, and glioblastoma

Processed data now available for 26 HCA 10x datasets

April 02, 2021

The HCA Data Portal 2.0 Preview now has standardized BAMs and count matrices ( Loom file format) available for 26 HCA projects, including 15 new projects. These projects contain both human and mouse single-cell and single-nucleus data generated with 3' 10x V2 and V3 sequencing technology. This data was processed using the latest version of the Optimus pipeline.

In addition to individual sample count matrices, each newly processed project also has standardized, project-level HCA Data Portal-generated matrices that are stratified by organ, species, and library construction method. These matrices are minimally filtered to include only cells with more than 100 UMIs. You can download the project-level HCA Data Portal generated Matrices from the Data Browser (see image below) or from the individual Project page (see the Exploring Projects guide)

HCA Data Portal Preview

New raw data and Contributor-Generated Matrices

Raw sequence files and contributor-generated matrices (CGMs) for an additional 11 new projects are available for download from the HCA Data Portal 2.0 Preview. These projects include human adult, embryonic, and fetal data derived from 10 organs - brain, blood, bone marrow, colon, thymus, pancreas, placenta, mouth, liver, and spleen. Most projects employed 10x sequencing technology, but some additionally used cite-seq and drop-seq.

With the addition of these new data, the HCA Data Portal now has 55 total projects with over 7 million cells derived from 40 organs and 580 donors. We are grateful for the contributions and continued support of the 179 global labs who made this data available.

Download new data using updated guides

All files (raw data, CGMs, and HCA Data Portal-generated BAMs and matrices) can be downloaded following the instructions in the Accessing HCA Data and Metadata guide. Additionally, you can access matrix files programmatically using the new Programmatic Download guide.

HCA Data Portal 2.0 launches; new projects, contributor generated matrices and HCA Data Portal 2.0 infrastructure

December 11, 2020

In the spirit of bringing HCA data to the community as quickly as possible, we are releasing the new HCA Data Portal 2.0 data and infrastructure incrementally.

This initial launch -- the first of several planned to roll out new functionality, pipelines, and data -- includes:

  • Raw data and standardized metadata for 5.8 million cells
  • Contributor-generated matrices, embeddings, and annotations for existing and 16 new HCA Data Portal projects
  • New HCA Data Portal 2.0 infrastructure (details below)

What's included in the new projects?

The new projects include a mix of human and mouse data from a variety of organs including adipose tissue, heart, hindlimb, spleen skin, yolk sac, diaphragm, tongue, trachea, and more. These data encompass:

  • 143 donors
  • 248 specimens
  • estimated 1.3M additional cells

What's included in the HCA Data Portal 2.0 infrastructure updates?

Along with the new data view, we have updated HCA Data Portal infrastructure by retiring and replacing the following features:

  • HCA Command Line Interface (CLI); data are now downloaded using curl commands (see the Accessing HCA Data and Metadata guide)
  • HCA Matrix Service; HCA Data Portal 1.0 project matrices remain available on the individual Project Matrices page (see the Exploring Projects guide)
  • HCA Data Storage Service (DSS) and API; data is now stored in the Terra Data Repo (TDR), an alternative storage and metadata management service that supports managed access

What's Coming Next?

Between now and the end of February look for:

  • Standardized analysis results (BAM and index files) made by the latest HCA 10x and SmartSeq-2 pipelines for all projects
  • HCA Data Portal-generated count matrices stratified by species, library construction method, and organ for each project

After these standardized analyses are complete, we will begin releasing new projects and analyses on a monthly basis. We are also working towards incorporating controlled-access projects.

Once processing is complete, we will retire HCA Data Portal 1.0 View.


Coming Soon - HCA Data Portal 2.0

October 9, 2020

We are excited to announce the launch of the HCA Data Portal 2.0 this fall. This has been a collaborative effort over the past 6 months to take on board the HCA community feedback and understand the unmet needs in order to align the goals of the HCA Data Portal with the wider HCA community goals.

We have made significant changes, including GA4GH-compliance, more data—50% more than previously—and, where available, contributor-generated count matrices, embeddings, and cell type annotations.

Changes Coming to Key Components

To accomplish this, we will be making the following changes and migrations:

  • The current Data Storage Service (DSS) will be retired and we will migrate to the Terra Data Repo, which supports managed access, for storage and metadata management. Both Ingest and the Data Browser will access the Terra Data Repo via self-service APIs, making for minimal disruption to the HCA scientific community.
  • The matrix service API will be retired. The per-project matrices that are most commonly used will be available in static form directly from the data browser.
  • As a higher-level replacement for the DSS API, the Data Browser API is being prepared for use by the wider developer community and will be officially documented and supported by the HCA Data Portal team.
  • The HCA-CLI will be retired and the Data Browser will provide a bulk download capability via curl (or similar) commands. Because the internal organization of the data store is subject to change with upcoming work on the metadata, direct calls against it are discouraged in favor of the new Data Browser API.

Transition Path to HCA Data Portal 2.0

More information about the transition to HCA Data Portal 2.0 will be announced in the coming weeks and we will endeavor to make this transition as seamless as possible to the HCA research and developer communities.

We will continue to integrate third-party portals and applications into the HCA ecosystem by linking from and integrating directly into the HCA Data Browser.

Regards,

The HCA Data Portal Team