May 11, 2023
Release Highlights
A Partial Picture of the Single-Cell Transcriptomics of Human IgA Nephropathy
Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways
Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
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.
Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts
Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant
Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses
Single-Cell RNA Sequencing in Multiple Pathologic Types of Renal Cell Carcinoma Revealed Novel Potential Tumor-Specific Markers
Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors
Spatially organized multicellular immune hubs in human colorectal cancer
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19
Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk
Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity
February 24, 2023
Release Highlights
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
Comprehensive cell atlas of the first-trimester developing human brain
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
Integrated analysis of multimodal single-cell data
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
Single-cell Transcriptome Atlas of Testis Aging
Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease
Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages
Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy
The single cell atlas of human endometrial stromal cells
Vento-tormo: Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk
Comparison of manual and two types of bioprinted kidney organoids by single cell RNA-seq
December 20, 2022
Release Highlights
A Single-Cell Transcriptome Atlas of Glia Diversity in the Human Hippocampus across the Lifespan and in Alzheimer’s Disease
A single-cell transcriptomic atlas of the human ciliary body
HCA seed network precise tumor-nephrectomy samples
Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing
Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior
Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord
Single-cell dissection of the human brain vasculature
Single-nuclei profiling of aged skeletal muscle
Single-nucleus transcriptomic atlas of spinal cord neuron in human
A single cell immune cell atlas of human hematopoietic system
Fate-mapping within human iPSC-derived kidney organoids reveals conserved mammalian nephron progenitor lineage relationships
Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells
RNA-Seq from human innate lymphoid cells (ILCs) transitional populations
Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition
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
Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types
Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium
SARS-CoV-2 infection of the oral cavity and saliva
Single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas
Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues
Single-Cell Lymphocyte Heterogeneity in Advanced Cutaneous T-cell Lymphoma Skin Tumors
Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma
Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons
The regulatory landscapes of human ovarian ageing
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
A single-cell reference map of transcriptional states for human blood and tissue T cell activation
October 19, 2022
Release Highlights
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Differential dynamics of response at single cell resolution following CAR-T therapy in refractory B-cell lymphoma
Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition
Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity
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
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!
A Single-Cell Characterization of Human Post-implantation Embryos Cultured In Vitro Delineates Morphogenesis in Primary Syncytialization
A Single-Cell Transcriptomic Atlas of Human Skin Aging
A human breast atlas integrating single-cell proteomics and transcriptomics
Defining Transcriptional Signatures of Human Hair Follicle Cell States
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
Mapping the developing human immune system across organs
Robust temporal map of human in vitro myelopoiesis using single-cell genomics
Single cell transcriptomics of human epidermis identifies basal stem cell transition states
Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord
Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
The myogenesis program drives clonal selection and drug resistance in rhabdomyosarcoma
Single-cell RNA-Seq reveals a developmental atlas of human prefrontal cortex
Profiling of transcribed cis-regulatory elements in single cells
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
Spatial multi-omic map of human myocardial infarction
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
August 23, 2022
Release Highlights
CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo
Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds
Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas
Single Cell Transcriptomics Reveals Cell Type Specific Diversification in Human Heart Failure
Single-cell Transcriptome Atlas of the Human Corpus Cavernosum
The immune cell atlas of human neuroblastoma
A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure
A cellular census of human lungs identifies novel cell states in health and in asthma
A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
Assessing the relevance of organoids to model inter-individual variation
Blood and immune development in human fetal bone marrow and Down syndrome
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)
Decoding Human Megakaryocyte Development
Developmental cell programs are co-opted in inflammatory skin disease
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
Molecular Architecture of the Mouse Nervous System
Molecular and functional heterogeneity of IL-10-producing CD4+ T cells
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Profiling of transcribed cis-regulatory elements in single cells
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
Sampling time-dependent artifacts in single-cell genomics studies
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
Single Cell RNAseq of primary pulmonary endothelial cells
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder
Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations
Spatial multi-omic map of human myocardial infarction
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
The Human and Mouse Enteric Nervous System at Single-Cell Resolution
Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition
July 19, 2022
Release Highlights
Lineage recording in human cerebral organoids
Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
The local and systemic response to SARS-CoV-2 infection in children and adults
Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks
A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing
Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue
Spatial multi-omic map of human myocardial infarction
June 29, 2022
Release Highlights
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors
Decoding Human Megakaryocyte Development
Memory-like natural killer cells facilitate effector functions of daratumumab in multiple myeloma
Profiling of transcribed cis-regulatory elements in single cells
Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor
Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies
Single-cell deciphering of human fetal innate lymphoid cell development
Single-cell sequencing unveils the heterogeneity of nonimmune cells in chronic apical periodontitis
The Human and Mouse Enteric Nervous System at Single-Cell Resolution
scRNA-seq experiments on human foreskin fibroblasts, foreskin fibroblasts induced directly to retina pigment epithelium, and induced pluripotent stem cell derived retina pigment epithelium
Assessing the relevance of organoids to model inter-individual variation
A single cell atlas of human teeth
Blood and immune development in human fetal bone marrow and Down syndrome
Capturing human trophoblast development with naive pluripotent stem cells in vitro
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
Extreme heterogeneity of influenza virus infection in single cells
Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
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
Single Cell RNA-Seq profiling human embryonic kidney cortex cells
Single cell RNA-seq of HeLa CCL2
Single cell RNAseq of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)
Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2
Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Single-cell transcriptomics of normal pancreas, intraductal papillary mucinous neoplasm, and pancreatic adenosquamous carcinoma reveals the heterogeneous progression of pancreatic ductal and stromal cells
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Spatial multi-omic map of human myocardial infarction
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers
The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles
June 9, 2022
Release Highlights
A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors
A single-cell atlas of breast cancer cell lines to study tumour heterogeneity and drug response
CITE-seq of in vitro control and memory-like human NK cells
Combinatorial transcription factor profiles predict mature and functional human islet α and β cells
RNA-Seq from human innate lymphoid cells (ILCs) transitional populations
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease
Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity
Skin single cell universe identifies IL-1B/IL23A co-producing CD14+ type 3 dendritic cells in psoriasis
Spatial multi-omic map of human myocardial infarction
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue
Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation
April 20, 2022
Release Highlights
A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics
A single-cell transcriptome atlas of human early embryogenesis
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
Cells of the human intestinal tract mapped across space and time
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)
Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
Molecular signatures of inflammatory profile and B-cell function in SFTS patients
Retinal ganglion cell-specific genetic regulation in primary open angle glaucoma
Single cell RNA-seq of HeLa CCL2
Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)
Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2
Single cell transcriptome atlases of the developing mouse and human spinal cord
Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
Single-cell RNA-Seq reveals a developmental atlas of human prefrontal cortex
Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder
Single-nucleus transcriptomic profiles of glial cells in human dorsal root ganglion and spinal cord
Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution - scRNA-Seq
Blood and immune development in human fetal bone marrow and Down syndrome
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
A cell atlas of human thymic development defines T cell repertoire formation
A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
Decoding human fetal liver haematopoiesis
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
March 30, 2022
Release Highlights
A cellular census of human lungs identifies novel cell states in health and in asthma
A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
Conserved cell types with divergent features in human versus mouse cortex
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids
Molecular Architecture of the Mouse Nervous System
Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19-associated AKI
Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection
Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation
Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers
Microglia Require CD4 T Cells to Complete the Fetal-to-Adult Transition
Assessing the relevance of organoids to model inter-individual variation
Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres
February 14, 2022
Release Highlights
We've created a new slack channel for the DCP community! Join the channel, say hello, and follow for the latest announcements, updates, and opportunities to connect with fellow DCP users.
The Data Portal header has been updated to include new features:
A global search bar that allows users to search across Projects, Guides, Pipeline Docs, and Metadata Schema.
Direct links to the HCA Twitter, GitHub repository, and slack channel.
A multi-omics atlas of the human retina at single-cell resolution
Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Pseudo-temporal ordering of individual cells reveals regulators of differentiation
Single cell RNA sequencing of human failing heart
Single cell RNAseq analysis of the developmental trajectory of iPSC-derived tenocytes
Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development
Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration
Spatial and single-cell transcriptional landscape of human cerebellar development
The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors
New DCP Analysis (19):
Cryopreservation and post-thaw characterization of dissociated human islet cells
Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq
Melanoma infiltration of stromal and immune cells
Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 diabetic donors
Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)
Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors
Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma
Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury
Single-cell RNA-seq reveals heterogeneity within human pre-cDCs
Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease
Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations
Systematic comparative analysis of single cell RNA-sequencing methods
Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq
Transcriptomes of 1,529 individual cells from 88 human preimplantation embryos
December 20, 2021
Release Highlights
The Data Portal links to new portals and tools:
The Analysis Portal's section now includes the Teichmann lab's Cambridge Cell Atlas .
The Methods Packages section now lists the Li lab's Cumulus software.
The Data Portal header has been updated with a new link to the Updates page so that viewers can readily follow release notes and other community announcements.
There are two new managed access projects available in the Browser:
Three projects have new uniform matrices generated with the updated Optimus pipeline that includes STARsolo software:
Several new projects also include data generated with multiple sequencing modalities (i.e. CITE-seq, 10x 3', and scATAC):
A Single-Cell Atlas of the Human Healthy Airways
A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
A single-cell atlas of chromatin accessibility in the human genome
An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine
Blood and immune cell development in human fetal bone marrow and in Down syndrome
CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function
Co-evolution of tumor and immune cells during progression of multiple myeloma
Extreme heterogeneity of influenza virus infection in single cells
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
Identification of distinct synovial fibroblast subsets associated with pain and progression of knee osteoarthritis using single-cell RNA sequencing
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics
Modeling Hepatoblastoma: Identification of Distinct Tumor Cell Populations and Key Genetic Mechanisms through Single Cell Sequencing (scRNA-seq)
SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells
Sampling time-dependent artifacts in single-cell genomics studies
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
Single-cell ATAC sequencing reveals the mechanism of human breast cancer metastasis
Single-cell RNA sequencing of human femoral head in vivo
Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease
Single-cell sequencing unveils distinct immune microenvironment in human chronic pancreatitis
Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets
A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells
AIDA pilot data
Distinct microbial and immune niches of the human colon
Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
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
Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation trajectory
Stress-induced RNA–chromatin interactions promote endothelial dysfunction
November 11, 2021
Release Highlights
Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq
Cryopreservation and post-thaw characterization of dissociated human islet cells
Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease
Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells
Healthy human kidney cell type single cell RNA-seq data
Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Pro-inflammatory T helper 17 directly harms oligodendrocytes in neuroinflammation
Single Cell RNAseq of primary pulmonary endothelial cells
Single cell RNAseq of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia
Single-nucleus cross-tissue molecular reference maps to decipher disease gene function
AIDA pilot data
Single cell RNA sequencing of multiple myeloma II
October 13, 2021
Release Highlights
Project downloads are now available from the project page. Download the files directly to your local machine via curl or export them to the cloud-based bioinformatics platform Terra by selecting the download next to the new "Terra Workspace" icon.
A Single-cell Transcriptomic Atlas of Human Intervertebral Disc
A human cell atlas of fetal gene expression
COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis
Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells
Lifespan charactarization of the nasal mucosa
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Single cell RNA-seq of brain glioblastoma samples
Single cell RNA-sequencing on healthy and IPF lung mesenchymal cells
Single cell atlas of the healthy breast
Single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells
Single-cell analysis of Crohn's disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia
Single-cell atlas of human oral mucosa reveals a stromal-neutrophil axis in tissue immunity regulation
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 DCP Analysis (2)
Census of Immune Cells
Integrative computational analysis of the substantia nigra pars compacta and the locus coeruleus
A single cell atlas of human teeth
Capturing human trophoblast development with naive pluripotent stem cells in vitro
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Female]
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Male]
Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans
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
Single Cell RNA-Seq profiling human embryonic kidney cortex cells
Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
Single-Cell RNA-Seq Analysis of cells from human urine
Single-cell RNA sequencing of human nasal swab from healthy donors
Single-cell RNA-sequencing reveals the landscape of cervical cancer heterogeneity
Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
Single-cell reconstruction of follicular remodeling in the human adult ovary
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles
September 17, 2021
New Raw Data
The DCP has added raw data for the following 14 new projects:
A molecular single-cell lung atlas of lethal COVID-19
Capturing human trophoblast development with naive pluripotent stem cells in vitro
Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues
Fate-mapping within human iPSC-derived kidney organoids reveals conserved mammalian nephron progenitor lineage relationships
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Female]
Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation [Male]
Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk
Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans
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
Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
Single-Cell RNA-Seq Analysis of cells from human urine
Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease
The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles
Updated Data
The following 3 projects have updated files:
A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells
Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation trajectory
DCP now contains data for 14 million estimated cells
August 25, 2021
New Raw Data
The DCP has added raw data for the following 12 new projects:
AIDA pilot data
Comparison of manual and two types of bioprinted kidney organoids by single cell RNA-seq
Developmental cell programs are co-opted in inflammatory skin disease
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids
Single-cell RNA sequencing of human nasal swab from healthy donors
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse
Single-cell transcriptomics of East-Asian pancreatic islets cells
The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome
The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss
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:
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
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 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.
New Managed Access and Seed Network projects
July 23, 2021
The DCP 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 DCP.
Additionally, DCP 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
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.
HCA Seed Networks Projects
Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
Stress-induced RNA–chromatin interactions promote endothelial dysfunction
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:
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle
Single-cell reconstruction of follicular remodeling in the human adult ovary
Single Cell RNA-Seq profiling human embryonic kidney cortex cells
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
A single cell atlas of human teeth
Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids
Single-cell RNA sequencing of normal human kidney
Single-cell RNA-sequencing reveals the landscape of cervical cancer heterogeneity
Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
Molecular and functional heterogeneity of IL-10-producing CD4+ T cells
Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra
The emergent landscape of the mouse gut endoderm at single-cell resolution
Microglia Require CD4 T Cells to Complete the Fetal-to-Adult Transition
High throughput error corrected Nanopore single cell transcriptome sequencing
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 DCP 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 DCP 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 DCP 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 (see the Optimus Overview ).
In addition to individual sample count matrices, each newly processed project also has standardized, project-level DCP-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 DCP-generated Matrices from the Data Browser (see image below) or from the individual Project page (see the Exploring Projects guide)
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 DCP 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 DCP 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 DCP-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.
DCP 2.0 launches; new projects, contributor generated matrices and DCP 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 DCP 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 DCP projects
New DCP 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
View the new projects using the DCP 2.0 Data Preview
What's included in the DCP 2.0 infrastructure updates?
Along with the new data view, we have updated DCP 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; DCP 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
DCP-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 DCP 1.0 View.
Coming Soon - DCP 2.0
October 9, 2020
We are excited to announce the launch of the DCP 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 DCP 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 DCP 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 DCP 2.0
More information about the transition to DCP 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.
To enable a smooth transition, the DCP 1 data browser, APIs and data will remain available until January 1, 2021.
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 DCP Team