The paper associated with this table can be viewed here: [Article] (https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1417428/full)
Link to detailed Single-cell RNA-seq database table can be found here: https://docs.google.com/spreadsheets/d/1fJuOeglSEjBIJbPOSONIX-zleyIaLn2ukT6DCxOn2k4/edit#gid=0
Databases brief overview:
| # | Database | Year | PMID | Citations | URL | Web Interface | Number of studies / dataset | Number of donors / samples | Number of cells | Data source |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | White Adipose Atlas | 2022 | 35296864 | 297 | Link | Available | 1 | 9 | 28465 | Primary |
| 2 | Vasculature of Adult Brain | 2022 | 35084939 | 136 | Link | Available | 1 | 5 | 161336 | Primary |
| 3 | Human Tonsil Atlas | 2024 | 38301653 | 17 | Link | Not available | 1 | 17 | 556000 | Primary |
| 4 | Human Lung Cell Atlas | 2020 | 33208946 | 1096 | Link | Available | 1 | 3 | 75000 | Primary |
| 5 | Liver Cell Atlas | 2020 | 31292543 | 785 | Link | Available | 1 | 9 | 10000 | Primary |
| 6 | Liver Cell Atlas | 2022 | 35021063 | 374 | Link | Available | 1 | 5 | 167598 | Primary |
| 7 | Kidney Cell Atlas | 2019 | 31604275 | 315 | Link | Available | 1 | 20 | 40268 | Primary |
| 8 | Heart Cell Atlas | 2020 | 32971526 | 974 | Link | Available | 1 | 14 | 704296 | Primary |
| 9 | CorneaCellAtlas | 2021 | 33865984 | 104 | Link | Available | 1 | 4 | 21343 | Primary |
| 10 | Human Breast Cell Atlas | 2023 | 37380767 | 33 | Link | Available | 1 | 126 | 714331 | Primary |
| 11 | Organoid | 2019 | 31619793 | 547 | Link | Available | 1 | 43498 | Primary | |
| 12 | First-trimester Developing Human Brain | 2023 | 37824650 | 30 | Link | Available | 1 | 26 | 1665937 | Primary |
| 13 | HCA Bone Marrow | 2018 | 30243574 | 179 | Link | Available | 1 | 8 | 100000 | Primary |
| 14 | Human Cell Landscape | 2020 | 32214235 | 750 | Link | Available | 1 | 63 | 700,000 | Primary |
| 15 | Descartes | 2021 | 33184181 | 486 | Link | Available | 1 | 15 | 4,000,000 | Primary |
| 16 | Tabula Sapiens | 2022 | 35549404 | 417 | Link | Available | 1 | 15 | 500,000 | Primary |
| 17 | GTEXsinglecellatlas | 2022 | 35549429 | 201 | Link | Available | 1 | 16 | 209,126 | Primary |
| 18 | Kidney Single-Cell Atlas | 2020 | 32978267 | 121 | Link | Available | 1 | 4 | 17,136 | Primary |
| 19 | Kidney Tissue Atlas | 2023 | 37468583 | 161 | Link | Available | 1 | 93 | 584,843 | Primary |
| 20 | Covid19 Cell Atlas | 2021 | 33915569 | 586 | Link | Available | 1 | 32 | 106,792 | Primary |
| 21 | Lung Atlas of Lethal COVID-19 | 2022 | 33915568 | 458 | Link | Available | 1 | 19 | 116,314 | Primary |
| 22 | ddnetbio | 2019 | 31768052 | 636 | Link | Available | 1 | 6 | 13,214 | Primary |
| 23 | Breast Cancer single-cell Atlas | 2022 | 35361816 | 65 | Link | Available | 1 | 32 | 35,276 | Primary |
| 24 | Single Cell Breast Cancer | 2023 | 37158690 | 4 | Link | Available | 1 | 21 | 117,958 | Primary |
| # | Database | Year | PMID | Citations | URL | Web Interface | Number of studies / dataset | Number of donors / samples | Number of cells | Data source |
|---|---|---|---|---|---|---|---|---|---|---|
| 25 | GEO/SRA | 2013 | 23193258 | 8811 | link | Available | 112585 | Aggregated | ||
| 26 | scRNA-seq package | 2016 | NA | 0 | link | Not available | 61 | 1641896 | Aggregated | |
| 27 | Human Cell Atlas | 2017 | 29206104 | 1942 | link | Available | 437 | 8600 | 58500000 | Aggregated |
| 28 | scRNASeqDB | 2017 | 29206167 | 91 | link | Available | 38 | 13440 | 13440 | Aggregated |
| 29 | Single Cell Expression Atlas | 2018 | 31665515 | 475 | link | Available | 147 | 10505726 | Aggregated | |
| 30 | SCPortalen | 2018 | 29045713 | 51 | link | Available | 23 | 20761 | Aggregated | |
| 31 | SCDevDB | 2019 | 31611909 | 20 | link | Available | 38 | 13440 | Aggregated | |
| 32 | PanglaoDB | 2019 | 30951143 | 867 | link | Available | 305 | 1126580 | Aggregated | |
| 33 | HuBMAP | 2019 | 31597973 | 368 | link | Available | 2362 | 1843 | Aggregated | |
| 34 | Curated Database | 2020 | 33247933 | 174 | link | Not available | 1946 | 134393568 | Aggregated | |
| 35 | Human Protein Atlas | 2021 | 34321199 | 749 | link | Available | 14 | 174271 | Aggregated | |
| 36 | Single Cell Portal | 2021 | 37502904 | 8 | link | Available | 654 | 40699488 | Aggregated | |
| 37 | UCSC Cell Browser | 2021 | 34244710 | 127 | link | Available | 378 | Aggregated | ||
| 38 | gEAR | 2021 | 34172972 | 112 | link | Available | 1180 | Aggregated | ||
| 39 | DISCO | 2022 | 34791375 | 55 | link | Available | 1077 | 13998 | 61280618 | Aggregated |
| 40 | singleCellBase | 2023 | 37730627 | 3 | link | Available | 464 | 9158 | Aggregated | |
| 41 | SingleScan | 2023 | 38062357 | 0 | link | Available | 109 | 3077622 | Aggregated | |
| 42 | AgeAnno | 2023 | 36200838 | 14 | link | Available | 226 | 1298996 | Aggregated | |
| 43 | scBrainMap | 2023 | 37195696 | 2 | link | Available | 715 | 6577222 | Aggregated | |
| 44 | Human Transcriptome Cell Atlas | 2023 | 36130266 | 14 | link | Available | 19 | 24652615 | Aggregated | |
| 45 | Human Universal Single Cell Hub | 2023 | 36318258 | 10 | link | Available | 185 | 300000 | Aggregated | |
| 46 | Cellxgene | 2023 | NA | 54 | link | Available | 1284 | 85100000 | Aggregated | |
| 47 | SCInter | 2023 | 38125297 | 0 | link | Available | 115 | 1016 | Aggregated | |
| 48 | OrganoidDB | 2023 | 36271792 | 4 | link | Available | 145 | 670000 | Aggregated | |
| 49 | SC2sepsis | 2022 | 35980286 | 1 | link | Available | 71 | 232226 | Aggregated | |
| 50 | SC2disease | 2021 | 33010177 | 67 | link | Available | 946481 | Aggregated | ||
| 51 | Human Lung Cell Atlas | 2023 | 37291214 | 130 | Link | Available | 49 | 486 | 2,400,000 | Aggregated |
| 52 | Covid19cellatlas | 2020 | 32327758 | 2678 | Link | Available | 15 | Aggregated | ||
| 53 | SCovid | 2022 | 34634820 | 30 | Link | Not available | 21 | 1042227 | Aggregated | |
| 54 | scREAD | 2020 | 33241205 | 74 | Link | Available | 73 | 713,640 | Aggregated | |
| 55 | ssREAD | 2023 | 37745592 | 0 | Link | Available | 35 | 2,572,355 | Aggregated | |
| 56 | SCAD-Brain | 2023 | 37251804 | 4 | Link | Available | 21 | 359 | 1,564,825 | Aggregated |
| 57 | JingleBells | 2017 | 28416714 | 0 | Link | Available | 302 | Aggregated | ||
| 58 | EndoDB | 2019 | 30357379 | 78 | Link | Available | 360 | 5847 | Aggregated | |
| 59 | huARdb | 2022 | 34606616 | 9 | Link | Available | 215 | 444794 | Aggregated | |
| 60 | ABC portal | 2023 | 35920330 | 9 | Link | Available | 198 | 3878881 | Aggregated | |
| 61 | CancerSEA | 2019 | 30329142 | 505 | Link | Available | 74 | 93,475 | Aggregated | |
| 62 | scTIME | 2021 | 34117085 | 33 | Link | Available | 49 | 196273 | Aggregated | |
| 63 | TISCH | 2021 | 33179754 | 542 | Link | Available | 76 | 2,045,746 | Aggregated | |
| 64 | Compendium papers1 | 2021 | 34914499 | 485 | Link | Available | 37 | 316 | 397,810 | Aggregated |
| 65 | Tumor Immune Cell Atlas | 2021 | 34548323 | 99 | Link | Available | 16 | 217 | 500,000 | Aggregated |
| 66 | TMExplorer | 2022 | 36084081 | 9 | Link | Available | 48 | 1438299 | Aggregated | |
| 67 | cancerSCEM | 2022 | 34643725 | 52 | Link | Available | 28 | 638,341 | Aggregated | |
| 68 | Compendium papers2 | 2022 | 36333338 | 129 | Link | Available | 12 | 226 | 855,271 | Aggregated |
| 69 | IMMUcanDB | 2023 | 36459564 | 12 | Link | Available | 144 | 4474385 | Aggregated | |
| 70 | TISCH2 | 2023 | 36321662 | 82 | Link | Available | 190 | 6,297,320 | Aggregated | |
| 71 | Curated Cancer Atlas | 2023 | 37258682 | 51 | Link | Available | 77 | 2,591,545 | Aggregated | |
| 72 | Pan-cancer T cell atlas | 2023 | 37248301 | 54 | Link | Available | 27 | 670 | 656,742 | Aggregated |
| 73 | SCAR | 2024 | 37739405 | 2 | Link | Available | 190 | 11301352 | Aggregated | |
| 74 | scRNA-seq-ICB-cohorts | 2024 | 38328153 | 0 | Link | Available | 8 | 90270 | Aggregated |