HCA Data Portal
Immune Network

Immune Network

The HCA datasets below focus on the network's tissues and are potential source datasets for integrated atlases.

Project TitleSpeciesMethodAnatomical EntityDisease (Donor)Cell Count Est.
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Homo sapiens

2 library construction methods

blood

normal
2 diseases

836,148

A cell atlas of human thymic development defines T cell repertoire formation
2 species
4 library construction methods
2 anatomical entities
normal

250,000

A comprehensive single cell transcriptional landscape of human hematopoietic progenitors

Homo sapiens

inDrop

hematopoietic system

normal

Unspecified

A human cell atlas of fetal gene expression.

Homo sapiens

sci-RNA-seq3

14 anatomical entities
normal

4,062,965

A molecular cell atlas of the human lung from single-cell RNA sequencing
2 species
2 library construction methods
2 anatomical entities
normal
3 diseases

75,000

A single cell immune cell atlas of human hematopoietic system

Homo sapiens

3 library construction methods
3 anatomical entities

Unspecified

1,453,784

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors.
2 species
2 library construction methods
6 anatomical entities
6 diseases

216,490

A single-cell atlas of chromatin accessibility in the human genome

Homo sapiens

sci-RNA-seq

18 anatomical entities
normal

500,000

AIDA

Homo sapiens

4 library construction methods

blood

Unspecified

82,755

An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics.

Homo sapiens

10X 3' v2 sequencing

blood

HIV infectious disease

43,731

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
3 species
12 library construction methods
4 anatomical entities
normal

50,556

Blood and immune development in human fetal bone marrow and Down syndrome

Homo sapiens

9 library construction methods
4 anatomical entities
normal

trisomy 21

164,709

Bone marrow plasma cells from hip replacement surgeries

Homo sapiens

MARS-seq

hematopoietic system

osteoarthritis, hip

9,500

CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

Homo sapiens

3 library construction methods

blood

dengue disease

Unspecified

CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo

Homo sapiens

10x 3' v3

thymus

Abnormal heart morphology

17,089

CITE-seq of in vitro control and memory-like human NK cells

Homo sapiens

CITE-seq

blood

normal

Unspecified

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

Homo sapiens

2 library construction methods
2 anatomical entities
normal
44 diseases

1,460,000

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.

Homo sapiens

4 library construction methods
8 anatomical entities
5 diseases

106,792

Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

Homo sapiens

CITE-seq

blood

normal

20,000

Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids

Homo sapiens

2 library construction methods
2 anatomical entities
normal

510,000

Comparison, calibration, and benchmarking of high-throughput single cell RNA-Seq techniques for unbiased cell-type classification

Homo sapiens

2 library construction methods

blood

normal

42,704

Construction of A Human Cell Landscape by Single-cell mRNA-seq

Homo sapiens

Microwell-Seq

37 anatomical entities
normal
19 diseases

702,968

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Homo sapiens

6 library construction methods
10 anatomical entities
normal

357,211

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

Homo sapiens

10x immune profiling

blood

normal

17,887

Differential dynamics of response at single cell resolution following CAR-T therapy in refractory B-cell lymphoma

Homo sapiens

10x immune profiling

blood

B-cell neoplasm

602,577

Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq
2 species

Smart-seq2

5 anatomical entities
normal

1,318

Dissecting the protein and transcriptional responses of human immune cells to T cell and monocyte specific activation

Homo sapiens

CITE-seq

blood

Unspecified

250,000

Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.

Homo sapiens

6 library construction methods
5 anatomical entities

metastatic melanoma

114,455

Distinct microbial and immune niches of the human colon

Homo sapiens

5 library construction methods
2 anatomical entities
normal

1,522

Dynamic changes in human single cell transcriptional signatures during fatal sepsis

Homo sapiens

10x 3' v3

blood

normal

bacterial infectious disease with sepsis

27,685

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

Homo sapiens

Fluidigm C1-based library preparation

2 anatomical entities
normal

1,001

GM-CSF-producing T helper cells: a distinct subset of T helper cells.

Homo sapiens

10x 3' v3 sequencing

blood

normal

70,000

Genetic ancestry effects on the response to viral infection are pervasive but cell type specific

Homo sapiens

10x 3' v2

blood

normal

235,000

Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

Homo sapiens

10x immune profiling

3 anatomical entities
normal

inflammatory bowel disease

121,368

Human SARS-CoV-2 challenge resolves local and systemic response dynamics

Homo sapiens

2 library construction methods
2 anatomical entities

COVID-19

606,074

Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing

Homo sapiens

10x 5' transcription profiling

blood

normal

preeclampsia

80,429

Immune landscape of viral- and carcinogen-drived head and neck cancer

Homo sapiens

10X 3' v2 sequencing

2 anatomical entities
normal
11 diseases

126,000

Immune signatures underlying post-acute COVID-19 lung sequelae

Homo sapiens

2 library construction methods
2 anatomical entities
normal
3 diseases

27,167

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19

Homo sapiens

10x 3' v3 sequencing

blood

normal
2 diseases

59,572

Integrated analysis of multimodal single-cell data

Homo sapiens

2 library construction methods

blood

HIV infectious disease

8,617

Integrated multiomic characterization of congenital heart disease

Homo sapiens

3 library construction methods
2 anatomical entities
normal
22 diseases

157,273

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

Homo sapiens

2 library construction methods

thymus

congenital heart disease

72,278

Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis.

Homo sapiens

2 library construction methods
2 anatomical entities
2 diseases

65,326

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

Homo sapiens

10x 3' v2

2 anatomical entities
normal

450,118

Local and systemic responses to SARS-CoV-2 infection in children and adults

Homo sapiens

2 library construction methods
3 anatomical entities
normal
2 diseases

659,217

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.

Homo sapiens

3 library construction methods

blood

normal
22 diseases

358,930

Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer.

Homo sapiens

2 library construction methods
3 anatomical entities
2 diseases

270,000

Mapping the developing human immune system across organs
2 species
5 library construction methods
10 anatomical entities
normal

922,332

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics

Homo sapiens

2 library construction methods
2 anatomical entities

renal cell carcinoma (disease)

37,055

Melanoma infiltration of stromal and immune cells

Mus musculus

Smart-seq2

3 anatomical entities

melanoma (disease)

6,639

Memory-like natural killer cells facilitate effector functions of daratumumab in multiple myeloma

Homo sapiens

10x 3' v3

hematopoietic system

plasma cell myeloma

7,165

Molecular and functional heterogeneity of IL-10-producing CD4+ T cells.

Homo sapiens

10x 3' v2

blood

normal

4,438

Molecular signatures of inflammatory profile and B-cell function in SFTS patients

Homo sapiens

10x 3' v2

blood

normal

thrombocytopenia

25,799

Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer

Homo sapiens

Visium Spatial Gene Expression

2 anatomical entities
normal

pancreatic ductal adenocarcinoma

124,898

Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes

Homo sapiens

10x sequencing

blood

lupus erythematosus

43,200

Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis'

Homo sapiens

Smart-seq2

2 anatomical entities
normal

multiple sclerosis

11,724

Pathogen-induced tissue-resident memory T <sub>H</sub> 17 (T <sub>RM</sub> 17) cells amplify autoimmune kidney disease

Homo sapiens

CITE-seq

2 anatomical entities
2 diseases

32,593

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis

Homo sapiens

Smart-seq2

blood

normal

asymptomatic dengue

2,244

Profiling of CD34+ cells from human bone marrow to understand hematopoiesis

Homo sapiens

10x 3' v2

bone marrow

normal

1,500,000

Profiling of transcribed cis-regulatory elements in single cells.

Homo sapiens

6 library construction methods
3 anatomical entities
normal

60,443

Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.

Homo sapiens

Smart-seq2

2 anatomical entities
normal

455

Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds.

Homo sapiens

2 library construction methods

thymus

normal

11,425

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics

Homo sapiens

2 library construction methods
3 anatomical entities
normal

orofaciodigital syndrome VIII

70,000

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

Homo sapiens

2 library construction methods
5 anatomical entities
2 diseases

49,253

Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics
2 species

10X 3' v2 sequencing

2 anatomical entities
normal
5 diseases

100,000

Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level

Homo sapiens

10x 3' transcription profiling

2 anatomical entities
normal
2 diseases

200,615

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Homo sapiens

2 library construction methods

blood

normal
4 diseases

90,957

Single Cell RNA-Seq Analysis Reveals Fate Decision of Human Pre-cDC Determined by Transcription Factor Competition

Homo sapiens

Fluidigm C1-based library preparation

blood

normal

188

Single cell RNA sequencing of multiple myeloma II

Homo sapiens

2 library construction methods

hematopoietic system

plasma cell myeloma

1,511

Single cell RNAseq analysis of the developmental trajectory of iPSC-derived tenocytes

Homo sapiens

10x 3' v3

2 anatomical entities
normal

Unspecified

Single cell profiling of COVID-19 patients: an international data resource from multiple tissues

Homo sapiens

CITE-seq

blood

4 diseases

97,499

Single cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) from mice flown on Rodent Research Reference Mission-2 (RRRM-2)

Mus musculus

10x 3' v3

blood

normal

80,000

Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2

Mus musculus

10x 3' v3

spleen

normal

80,000

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.

Homo sapiens

3 library construction methods
3 anatomical entities
2 diseases

72,000

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells

Homo sapiens

Fluidigm C1-based library preparation

blood

normal

HIV infectious disease

224

Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy

Homo sapiens

STRT-seq

2 anatomical entities
normal
4 diseases

3,620

Single-cell ATAC sequencing reveals the mechanism of human breast cancer metastasis

Homo sapiens

10x scATAC-seq

immune organ

luminal B breast carcinoma

11,327

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

Homo sapiens

10x 3' v2

blood

normal

25,000

Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease

Homo sapiens

2 library construction methods

blood

normal

Alzheimer disease

36,849

Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human.

Homo sapiens

10X 3' v2 sequencing

3 anatomical entities

Unspecified

207,000

Single-cell RNA-seq in monozygotic twins discordant for multiple sclerosis

Homo sapiens

Smart-like

Immune system

normal
5 diseases

3,360

Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor

Homo sapiens

2 library construction methods

hematopoietic system

normal

aplastic anemia

20,000

Single-cell RNA-seq of human peripheral blood NKT cells

Homo sapiens

10X 3' v2 sequencing

blood

normal

14,119

Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus

Homo sapiens

10x 3' v2

blood

systemic lupus erythematosus

Unspecified

Single-cell RNA-seq reveals heterogeneity within human pre-cDCs

Homo sapiens

Smart-seq2

blood

normal

957

Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue.

Homo sapiens

2 library construction methods

blood vessel

normal
4 diseases

48,128

Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

Homo sapiens

10x 3' transcription profiling

2 anatomical entities

Crohn ileitis

Unspecified

Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

Homo sapiens

10X 3' v2

bone marrow

normal

childhood acute lymphoblastic leukemia

39,375

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

Homo sapiens

10x 5' v2

blood

normal

302,255

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

Homo sapiens

8 library construction methods
2 anatomical entities
4 diseases

361,929

Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment

Homo sapiens

2 library construction methods
5 anatomical entities
3 diseases

45,851

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

Homo sapiens

10x 5' v2

blood

normal

1,916,367

Single-cell deciphering of human fetal innate lymphoid cell development

Homo sapiens

10x 3' v3

6 anatomical entities
normal

Unspecified

Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease

Homo sapiens

10x 3' v2

blood

normal

1,267,758

Single-cell multi-omics analysis of the immune response in COVID-19

Homo sapiens

4 library construction methods

blood

normal
5 diseases

800,000

Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals

Homo sapiens

2 library construction methods

blood

normal

COVID-19

124,726

Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease

Homo sapiens

Smart-seq2

blood

Unspecified

221

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.

Homo sapiens

2 library construction methods
3 anatomical entities
2 diseases

167,283

Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms of homing for neutrophils

Homo sapiens

10x v2 sequencing

lymph node

3 diseases

33,000

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

Homo sapiens

2 library construction methods
15 anatomical entities
normal

84,363