| A blood atlas of COVID-19 defines hallmarks of disease severity and specificity | Homo sapiens | 2 library construction methods | blood | | 836,148 |
| A cell atlas of human thymic development defines T cell repertoire formation | 2 species | 4 library construction methods | 2 anatomical entities | | 250,000 |
| A comprehensive single cell transcriptional landscape of human hematopoietic progenitors | Homo sapiens | inDrop | hematopoietic system | | Unspecified |
| A human cell atlas of fetal gene expression. | Homo sapiens | sci-RNA-seq3 | 14 anatomical entities | | 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 | | 75,000 |
| A single cell immune cell atlas of human hematopoietic system | Homo sapiens | 3 library construction methods | 3 anatomical entities | | 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 | | 216,490 |
| A single-cell atlas of chromatin accessibility in the human genome | Homo sapiens | sci-RNA-seq | 18 anatomical entities | | 500,000 |
| A spatial human thymus cell atlas mapped to a continuous tissue axis | Homo sapiens | 6 library construction methods | thymus | | Unspecified |
| AIDA | Homo sapiens | 4 library construction methods | blood | | 82,755 |
| An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics. | Homo sapiens | 10X 3' v2 sequencing | blood | | 43,731 |
| Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects | 3 species | 12 library construction methods | 4 anatomical entities | | 50,556 |
| Blood and immune development in human fetal bone marrow and Down syndrome | Homo sapiens | 9 library construction methods | 4 anatomical entities | | 164,709 |
| Bone marrow plasma cells from hip replacement surgeries | Homo sapiens | MARS-seq | hematopoietic system | | 9,500 |
| CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function | Homo sapiens | 3 library construction methods | blood | | 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 | | Unspecified |
| COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. | Homo sapiens | 2 library construction methods | 2 anatomical entities | | 1,460,000 |
| COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. | Homo sapiens | 4 library construction methods | 8 anatomical entities | | 106,792 |
| Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | Homo sapiens | CITE-seq | blood | | 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 | | 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 | | 42,704 |
| Construction of A Human Cell Landscape by Single-cell mRNA-seq | Homo sapiens | Microwell-Seq | 37 anatomical entities | | 702,968 |
| Cross-tissue immune cell analysis reveals tissue-specific features in humans | Homo sapiens | 6 library construction methods | 10 anatomical entities | | 357,211 |
| Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins | Homo sapiens | 10x immune profiling | blood | | 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 | | 602,577 |
| Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq | 2 species | Smart-seq2 | 5 anatomical entities | | 1,318 |
| Dissecting the protein and transcriptional responses of human immune cells to T cell and monocyte specific activation | Homo sapiens | CITE-seq | blood | | 250,000 |
| Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. | Homo sapiens | 6 library construction methods | 5 anatomical entities | | 114,455 |
| Distinct microbial and immune niches of the human colon | Homo sapiens | 5 library construction methods | 2 anatomical entities | | 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 | | 1,001 |
| GM-CSF-producing T helper cells: a distinct subset of T helper cells. | Homo sapiens | 10x 3' v3 sequencing | blood | | 70,000 |
| Genetic ancestry effects on the response to viral infection are pervasive but cell type specific | Homo sapiens | 10x 3' v2 | blood | | 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 | | 606,074 |
| Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing | Homo sapiens | 10x 5' transcription profiling | blood | | 80,429 |
| Immune landscape of viral- and carcinogen-drived head and neck cancer | Homo sapiens | 10X 3' v2 sequencing | 2 anatomical entities | | 126,000 |
| Immune signatures underlying post-acute COVID-19 lung sequelae | Homo sapiens | 2 library construction methods | 2 anatomical entities | | 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 | | 59,572 |
| Integrated analysis of multimodal single-cell data | Homo sapiens | 2 library construction methods | blood | | 8,617 |
| Integrated multiomic characterization of congenital heart disease | Homo sapiens | 3 library construction methods | 2 anatomical entities | | 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 | | 72,278 |
| Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. | Homo sapiens | 2 library construction methods | 2 anatomical entities | | 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 | | 450,118 |
| Local and systemic responses to SARS-CoV-2 infection in children and adults | Homo sapiens | 2 library construction methods | 3 anatomical entities | | 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 | | 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 | | 270,000 |
| Mapping the developing human immune system across organs | 2 species | 5 library construction methods | 10 anatomical entities | | 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 | | 6,639 |
| Memory-like natural killer cells facilitate effector functions of daratumumab in multiple myeloma | Homo sapiens | 10x 3' v3 | hematopoietic system | | 7,165 |
| Molecular and functional heterogeneity of IL-10-producing CD4+ T cells. | Homo sapiens | 10x 3' v2 | blood | | 4,438 |
| Molecular signatures of inflammatory profile and B-cell function in SFTS patients | Homo sapiens | 10x 3' v2 | blood | | 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 | | 43,200 |
| Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis' | Homo sapiens | Smart-seq2 | 2 anatomical entities | | 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 | | 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 | | 1,500,000 |
| Profiling of transcribed cis-regulatory elements in single cells. | Homo sapiens | 6 library construction methods | 3 anatomical entities | | 60,443 |
| Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation. | Homo sapiens | Smart-seq2 | 2 anatomical entities | | 455 |
| Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds. | Homo sapiens | 2 library construction methods | thymus | | 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 | | 49,253 |
| Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics | 2 species | 10X 3' v2 sequencing | 2 anatomical entities | | 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 | | 200,615 |
| Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment | Homo sapiens | 2 library construction methods | blood | | 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 | | 188 |
| Single cell RNA sequencing of multiple myeloma II | Homo sapiens | 2 library construction methods | hematopoietic system | | 1,511 |
| Single cell RNAseq analysis of the developmental trajectory of iPSC-derived tenocytes | Homo sapiens | 10x 3' v3 | 2 anatomical entities | | Unspecified |
| Single cell profiling of COVID-19 patients: an international data resource from multiple tissues | Homo sapiens | CITE-seq | blood | | 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 | | 80,000 |
| Single cell transcriptional profiling of spleens from mice flown on Rodent Research Reference Mission-2 | Mus musculus | 10x 3' v3 | spleen | | 80,000 |
| Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. | Homo sapiens | 3 library construction methods | 3 anatomical entities | | 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 | | 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 demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma | Homo sapiens | 10x 3' v2 | 4 anatomical entities | | 208,506 |
| Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs | Homo sapiens | 10x 3' v2 | blood | | 25,000 |
| Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease | Homo sapiens | 2 library construction methods | blood | | 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 | | 207,000 |
| Single-cell RNA-seq in monozygotic twins discordant for multiple sclerosis | Homo sapiens | Smart-like | Immune system | | 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 | | 20,000 |
| Single-cell RNA-seq of human peripheral blood NKT cells | Homo sapiens | 10X 3' v2 sequencing | blood | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 1,916,367 |
| Single-cell deciphering of human fetal innate lymphoid cell development | Homo sapiens | 10x 3' v3 | 6 anatomical entities | | Unspecified |
| Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease | Homo sapiens | 10x 3' v2 | blood | | 1,267,758 |
| Single-cell multi-omics analysis of the immune response in COVID-19 | Homo sapiens | 4 library construction methods | blood | | 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 | | 124,726 |
| Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease | Homo sapiens | Smart-seq2 | blood | | 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 | | 167,283 |
