| A cell atlas of human thymic development defines T cell repertoire formation | 2 species | 4 library construction methods | 2 anatomical entities | | 250,000 |
| A human cell atlas of fetal gene expression. | Homo sapiens | sci-RNA-seq3 | 14 anatomical entities | | 4,062,965 |
| A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics | Homo sapiens | 10x 3' v3 | 2 anatomical entities | | 12,590 |
| A single-cell atlas of chromatin accessibility in the human genome | Homo sapiens | sci-RNA-seq | 18 anatomical entities | | 500,000 |
| An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine | Homo sapiens | 2 library construction methods | 5 anatomical entities | | Unspecified |
| Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn’s Disease | Homo sapiens | 10x 5' v1 | ileum | | 139,906 |
| Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects | 3 species | 12 library construction methods | 4 anatomical entities | | 50,556 |
| Cells of the human intestinal tract mapped across space and time | Homo sapiens | 2 library construction methods | 4 anatomical entities | normal type 2 diabetes mellitus | 428,000 |
| Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease. | Homo sapiens | 10X 3' v2 sequencing | digestive system | normal ulcerative colitis (disease) | 11,175 |
| 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 |
| Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps | Homo sapiens | TruDrop | colon | | 68,301 |
| Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells | Homo sapiens | 2 library construction methods | 3 anatomical entities | | Unspecified |
| Distinct microbial and immune niches of the human colon | Homo sapiens | 5 library construction methods | 2 anatomical entities | | 1,522 |
| Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition | Homo sapiens | 2 library construction methods | 3 anatomical entities | normal type 2 diabetes mellitus | 36,487 |
| 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 |
| Identification of a unique subset of tissue-resident memory CD4+ T cells in Crohn’s disease | Homo sapiens | 2 library construction methods | 2 anatomical entities | | 25,171 |
| Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. | Homo sapiens | 2 library construction methods | 7 anatomical entities | | 366,650 |
| Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. | Homo sapiens | 10x 3' v2 | large intestine | | 109,512 |
| Mapping Development of the Human Intestinal Niche at Single-Cell Resolution | Homo sapiens | 2 library construction methods | small intestine | | Unspecified |
| Mapping the developing human immune system across organs | 2 species | 5 library construction methods | 10 anatomical entities | | 922,332 |
| Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy | Homo sapiens | 2 library construction methods | colon | | 119,578 |
| Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways | Homo sapiens | 3 library construction methods | colon | | 73,165 |
| 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 |
| Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas | Homo sapiens | 10x 5' transcription profiling | colon | | 49,589 |
| SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. | 2 species | 4 library construction methods | 4 anatomical entities | | 33,844 |
| Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues | Homo sapiens | 2 library construction methods | 3 anatomical entities | | 122,000 |
| Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease | Homo sapiens | SORT-seq | small intestine | | 4,000 |
| Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer | Homo sapiens | 10x TCR enrichment | 2 anatomical entities | | 200,000 |
| Single-Cell Transcriptome and Downstream Analyses of Human Stomach Reveal the Cell Diversity and Developmental Features of Gastric and Metaplastic Mucosae | Homo sapiens | 2 library construction methods | stomach | | 137,610 |
| Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions | Homo sapiens | 10x 3' v3 | 2 anatomical entities | | 29,247 |
| 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 gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity | Homo sapiens | 10x 3' v2 | stomach | | 13,022 |
| 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 deciphering of human fetal innate lymphoid cell development | Homo sapiens | 10x 3' v3 | 6 anatomical entities | | Unspecified |
| Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs | Homo sapiens | 2 library construction methods | 15 anatomical entities | | 84,363 |
| Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. | Homo sapiens | 4 library construction methods | 8 anatomical entities | | 220,527 |
| Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. | Homo sapiens | 10x 3' v2 | 7 anatomical entities | | 209,126 |
| Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations | Homo sapiens | Smart-seq2 | abdomen | | 184 |
| Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers | Homo sapiens | 10x 3' v2 | stomach | | 30,365 |
| Spatially organized multicellular immune hubs in human colorectal cancer | Homo sapiens | 2 library construction methods | colon | colorectal adenocarcinoma | 371,223 |
| Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution - scRNA-Seq | Homo sapiens | 2 library construction methods | 3 anatomical entities | | 98,866 |
| Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease | 2 species | 2 library construction methods | colon | | 16,893 |
| Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution | Mus musculus | Smart-seq2 | 18 anatomical entities | | 100,605 |
| The Human and Mouse Enteric Nervous System at Single-Cell Resolution. | 2 species | 2 library construction methods | 2 anatomical entities | | 1,600,000 |
| The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss | Homo sapiens | 10x 3' v3 sequencing | decidua | | 14,000 |
| The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans | Homo sapiens | 3 library construction methods | 24 anatomical entities | | 481,120 |
| The emergent landscape of the mouse gut endoderm at single-cell resolution | Mus musculus | 10x 3' v2 | 3 anatomical entities | | 112,201 |
| The immune cell atlas of human neuroblastoma | Homo sapiens | 10x 3' v2 | 7 anatomical entities | | 46,261 |
| The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon | Homo sapiens | 3 library construction methods | 3 anatomical entities | | 720,633 |
| The myogenesis program drives clonal selection and drug resistance in rhabdomyosarcoma | Homo sapiens | 5 library construction methods | 12 anatomical entities | | 764,251 |
| Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity | Homo sapiens | 10x 3' v2 | colon | normal inflammatory bowel disease | 40,327 |
| scRNA-Seq Reveals New Enteric Nervous System Roles for GDNF, NRTN, and TBX3 | 2 species | 10x 3' v2 | 2 anatomical entities | | 11,944 |
| scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation | Homo sapiens | 3 library construction methods | 3 anatomical entities | | 199,845 |
