| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | AC | AD | AE | AF | AG | AH | AI | AJ | AK | AL | AM | AN | AO | AP | AQ | AR | AS | AT | AU | AV | AW | AX | AY | AZ | BA | BB | BC | BD | BE | BF | BG | BH | BI | BJ | BK | BL | BM | BN | BO | BP | BQ | BR | BS | BT | BU | BV | BW | BX | BY | BZ | CA | CB | CC | CD | CE | CF | CG | CH | CI | CJ | CK | CL | CM | CN | CO | CP | CQ | CR | CS | CT | CU | CV | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Atlas | Network | Wave | Source Study | DOI | Task | Title | Task Type | Status | Target Completion | Created At | Completed At | UUID | gh_ticket | in_lists | doi url | ingest url | wrangling state | STATE | azup shortname | azul fastq | Notes | Accession | ingest data | ingest data notes | ingest wrangling notes | metadata spreadsheet | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | Adipose v1.0 | adipose | 3 | Hinte (2024) Nature | 10.1038/s41586-024-08165-7 | Ingest source study. | Adipose tissue retains an epigenetic memory of obesity after weight loss | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-02-25T13:43:22.529Z | 8913bc18-966d-4507-9259-1a7c9f6bef1c | 0 | https://doi.org/10.1038/s41586-024-08165-7 | https://contribute.data.humancellatlas.org/projects/detail?uuid=8913bc18-966d-4507-9259-1a7c9f6bef1c&tab=data | Stalled | stalled | GSE236580 | It's complicated | Human snRNA-seq data from the MTSS and LTSS cohorts are available upon request from C.W. and M.B. Human snRNA-seq data from the NEFA cohort are available upon request from F.v.M., N.K. and M.R | Part of adipose list. Human data available upon request | https://explore.data.humancellatlas.org/projects/8913bc18-966d-4507-9259-1a7c9f6bef1c/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | Adipose v1.0 | adipose | 3 | Tong and Liu et al, bliu@nus.edu.sg - Unpublished | Unpublished | Ingest source study. | Tong_Lui_unpubl | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-02-25T13:36:35.337Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 | Breast v1.0 | breast | 3 | Kumar (2023) Nature | 10.1038/s41586-023-06252-9 | Ingest source study. | A spatially resolved single-cell genomic atlas of the adult human breast | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-06-20T17:20:20.305Z | 2024-06-20T17:20:21.628Z | 1ffa2223-28a6-4133-a5a4-badd00faf4bc | 0 | https://doi.org/10.1038/s41586-023-06252-9 | https://contribute.data.humancellatlas.org/projects/detail?uuid=1ffa2223-28a6-4133-a5a4-badd00faf4bc&tab=data | lattice | lattice | Aspatiallyresolvedsingle-cellgenomicatlasoftheadul | TRUE | lattice | GSE195665; GSE234817; GSE235326; GSE234814; PRJNA801681; PRJNA983286; PRJNA985695; PRJNA983280; SRP443155; SRP445031; SRP443363 | #ERROR! | #ERROR! | #ERROR! | https://explore.data.humancellatlas.org/projects/1ffa2223-28a6-4133-a5a4-badd00faf4bc/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 | Adipose v1.0 | adipose | 3 | AlZaim (2024) bioRxiv | 10.1101/2024.09.22.610444 | Ingest source study. | Defining the Vascular Niche of Human Adipose Tissue Across Metabolic Conditions | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-02-25T13:38:38.206Z | f67ed416-874e-411d-b34e-aff672377cf2 | 0 | https://doi.org/10.1101/2024.09.22.610444 | https://contribute.data.humancellatlas.org/projects/detail?uuid=f67ed416-874e-411d-b34e-aff672377cf2&tab=data | Stalled | stalled | GSE268904 | It's complicated | Accession "GSE268904" is currently private and is scheduled to be released on Jun 30, 2025. UPDATE: to be released on Dec 31, 2025. | Part of adipose list. GEO data to be released on Dec 31, 2025. | https://explore.data.humancellatlas.org/projects/f67ed416-874e-411d-b34e-aff672377cf2/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
6 | Gut v1.0 | gut | 1 | Maddipatla (2022) Inflammatory Bowel Diseases | 10.1093/ibd/izac201 | Ingest source study. | Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn’s Disease | INGEST | DONE | 2024-12-31T23:59:59.999Z | 2024-05-28T21:35:20.694Z | 2024-09-26T17:05:10.087Z | 9dd91b6e-7c62-49d3-a3d4-74f603deffdb | 0 | https://doi.org/10.1093/ibd/izac201 | https://contribute.data.humancellatlas.org/projects/detail?uuid=9dd91b6e-7c62-49d3-a3d4-74f603deffdb&tab=data | Submitted | wrangled | diversityOfIlealMucosa | TRUE | QiuLab? | GSE202052 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/9dd91b6e-7c62-49d3-a3d4-74f603deffdb/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
7 | Heart v1.0 | heart | 2 | Koenig (2022) Nature Cardiovascular Research | 10.1038/s44161-022-00028-6 | Ingest source study. | Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:51.094Z | 2024-05-20T07:03:51.102Z | 135f7f5c-4a85-4bcf-9f7c-4f035ff1e428 | 1 | https://doi.org/10.1038/s44161-022-00028-6 | https://contribute.data.humancellatlas.org/projects/detail?uuid=135f7f5c-4a85-4bcf-9f7c-4f035ff1e428&tab=data | Published in DCP | wrangled | humanHeartFailureCellularLandscape | TRUE | SRP336428; GSE183852; PRJNA762100 | All fully open | #REF! | Wrangler: Britney 19June24 AC: added peer-reviewed publication | https://explore.data.humancellatlas.org/projects/135f7f5c-4a85-4bcf-9f7c-4f035ff1e428/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8 | MSK v1.0 | musculoskeletal | 3 | Elisabet Stener-Victorin, elisabet.stener-victorin@ki.se - Unpublished | Unpublished | Ingest source study. | PIAII | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T07:55:05.330Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
9 | Reproduction v1.0 | reproduction | 3 | Pique-Regi (2022) JCI Insight | 10.1172/jci.insight.153921 | Ingest source study. | A single-cell atlas of the myometrium in human parturition | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-03-31T16:38:09.691Z | d1dc95a0-bcf4-4f91-af5f-d6e0a722cd95 | 0 | https://doi.org/10.1172/jci.insight.153921 | https://contribute.data.humancellatlas.org/projects/detail?uuid=d1dc95a0-bcf4-4f91-af5f-d6e0a722cd95&tab=data | Stalled | stalled | phs001886.v4.p1 | All managed access | no file is accessible, all under MA in phs001886.v4.p1 | No public data could be found. | https://explore.data.humancellatlas.org/projects/d1dc95a0-bcf4-4f91-af5f-d6e0a722cd95/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
10 | Immune v1.0 | immune | 1 | Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia (2020) medRxiv | 10.1101/2020.11.20.20227355 | Ingest source study. | Single cell profiling of COVID-19 patients: an international data resource from multiple tissues | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:48.203Z | 2024-05-20T07:03:48.284Z | 2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba | 1 | https://doi.org/10.1101/2020.11.20.20227355 | https://contribute.data.humancellatlas.org/projects/detail?uuid=2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba&tab=data | Published in DCP | wrangled | COVID19autoimmunityPBMCs | FALSE | raw not available/managed access | A mixture of open and managed | #REF! | https://explore.data.humancellatlas.org/projects/2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11 | ORCF v1.0 | oral | 2 | Huang (2021) Nature Medicine | 10.1038/s41591-021-01296-8 | Ingest source study. | SARS-CoV-2 infection of the oral cavity and saliva | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-28T19:37:11.096Z | 2024-05-28T19:37:11.413Z | dcbb50d1-9acf-4f70-9fda-b1f63a948c49 | #829 | 2 | https://doi.org/10.1038/s41591-021-01296-8 | https://contribute.data.humancellatlas.org/projects/detail?uuid=dcbb50d1-9acf-4f70-9fda-b1f63a948c49&tab=data | Published in DCP | wrangled | SARS-CoV-2InfectionOralCavity | FALSE | raw not available | All fully open | #REF! | Uploaded for project catalogue | https://explore.data.humancellatlas.org/projects/dcbb50d1-9acf-4f70-9fda-b1f63a948c49/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
12 | Lung v1.0 | lung | 1 | Schiller - Unpublished | Unpublished | Ingest source study. | Schiller_2021 | INGEST | TODO | 2024-09-30T23:59:59.999Z | 2024-05-28T23:08:50.758Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
13 | Lung v1.0 | lung | 1 | Wauters (2021) Cell Research | 10.1038/s41422-020-00455-9 | Ingest source study. | Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:43.094Z | 2024-05-20T07:03:43.101Z | 92892ab2-1334-4b1c-9761-14f5a73548ea | 1 | https://doi.org/10.1038/s41422-020-00455-9 | https://contribute.data.humancellatlas.org/projects/detail?uuid=92892ab2-1334-4b1c-9761-14f5a73548ea&tab=data | Published in DCP | wrangled | BALDiscriminatingCOVID-19 | FALSE | raw managed access EGAS00001004717 | EGAS00001004717 | A mixture of open and managed | read count matrix available at https://lambrechtslab.sites.vib.be/en/immune-atlas | Imported from nxn db 2021-10-12 | https://explore.data.humancellatlas.org/projects/92892ab2-1334-4b1c-9761-14f5a73548ea/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
14 | Adipose v1.0 | adipose | 3 | Emont (2022) Nature | 10.1038/s41586-022-04518-2 | Ingest source study. | A single-cell atlas of human and mouse white adipose tissue | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-30T07:30:03.197Z | 2025-04-17T11:10:01.801Z | fc2a0b4e-1e4a-447b-a097-47b398402f37 | 0 | https://doi.org/10.1038/s41586-022-04518-2 | https://contribute.data.humancellatlas.org/projects/detail?uuid=fc2a0b4e-1e4a-447b-a097-47b398402f37&tab=data | Submitted | wrangled | HumanMouseWhiteAdipose | FALSE | core dataset | SRP322736; phs002766.v1; GSE176067; GSE176171; PRJNA734779; PRJNA735210 | All fully open | Analysis files in SCP1376, raw human matrices phs002766.v1 | Part of Adipose v1.0 | https://explore.data.humancellatlas.org/projects/fc2a0b4e-1e4a-447b-a097-47b398402f37/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
15 | Kidney v1.0 | kidney | 1 | Krishna (2021) Cancer Cell | 10.1016/j.ccell.2021.03.007 | Ingest source study. | Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:49.386Z | 2024-05-20T07:03:49.483Z | 12f32054-8f18-4dae-8959-bfce7e3108e7 | #996 | 1 | https://doi.org/10.1016/j.ccell.2021.03.007 | https://contribute.data.humancellatlas.org/projects/detail?uuid=12f32054-8f18-4dae-8959-bfce7e3108e7&tab=data | Published in DCP | wrangled | ImmuneLandscapeccRCC | TRUE | PRJNA705464 | All fully open | #REF! | 091122: Added for Kidney Atlas. | https://explore.data.humancellatlas.org/projects/12f32054-8f18-4dae-8959-bfce7e3108e7/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
16 | Organoid-Endoderm v1.0 | organoid | 3 | Lee (2021) Nature Communications | 10.1038/s41467-021-24746-w | Ingest source study. | Development of a quantitative prediction algorithm for target organ-specific similarity of human pluripotent stem cell-derived organoids and cells | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:05:17.533Z | #N/A | 0 | https://doi.org/10.1038/s41467-021-24746-w | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
17 | Organoid-Neural v1.0 | organoid | 3 | Sawada (2020) Molecular Psychiatry | 10.1038/s41380-020-0844-z | Ingest source study. | Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T07:45:24.198Z | #N/A | 0 | https://doi.org/10.1038/s41380-020-0844-z | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
18 | Liver v1.0 | liver | 2 | Narmada (2024) Journal of Hepatology | 10.1016/j.jhep.2024.02.017 | Ingest source study. | Single cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity | INGEST | DONE | 2024-12-31T23:59:59.999Z | 2024-05-28T19:25:23.804Z | 2025-04-17T11:10:02.556Z | 38e34131-62fc-4323-b435-15113dfd6dcc | 0 | https://doi.org/10.1016/j.jhep.2024.02.017 | https://contribute.data.humancellatlas.org/projects/detail?uuid=38e34131-62fc-4323-b435-15113dfd6dcc&tab=data | Submitted | wrangled | CuredChronicHepatitisNarmada | TRUE | Very recent publication, likely added to the list recently or substituting one of the unpublished ones? | SRP499879; PRJNA1096305 | All fully open | #REF! | Part of Liver v1.0 | https://explore.data.humancellatlas.org/projects/38e34131-62fc-4323-b435-15113dfd6dcc/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
19 | Lung v1.0 | lung | 1 | Vieira Braga (2019) Nature Medicine | 10.1038/s41591-019-0468-5 | Ingest source study. | A cellular census of human lungs identifies novel cell states in health and in asthma | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:42.182Z | 2024-05-20T07:03:42.192Z | c0518445-3b3b-49c6-b8fc-c41daa4eacba | #537 | 2 | https://doi.org/10.1038/s41591-019-0468-5 | https://contribute.data.humancellatlas.org/projects/detail?uuid=c0518445-3b3b-49c6-b8fc-c41daa4eacba&tab=data | Published in DCP | wrangled | lungCellularCensus | FALSE | raw not available/managed access EGAS00001001755/ GSE130148 | EGAS00001001755; EGAS00001002649; GSE130148 | A mixture of open and managed | #REF! | https://explore.data.humancellatlas.org/projects/c0518445-3b3b-49c6-b8fc-c41daa4eacba/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
20 | MSK v1.0 | musculoskeletal | 3 | Hanks (2025) Cell Genomics | 10.1016/j.xgen.2025.100915 | Ingest source study. | Extensive differential gene expression and regulation by sex in human skeletal muscle | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-08-19T10:13:18.812Z | 6f309fdf-cf56-4078-a936-eeded8fc6bdf | 0 | https://doi.org/10.1016/j.xgen.2025.100915 | https://contribute.data.humancellatlas.org/projects/detail?uuid=6f309fdf-cf56-4078-a936-eeded8fc6bdf&tab=data | New | not wrangled | All managed access | 040925: No file available online, MA in phs001048.v3.p1 | Part of MSK v1.0; no files to ingest | https://explore.data.humancellatlas.org/projects/6f309fdf-cf56-4078-a936-eeded8fc6bdf/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
21 | Lung v1.0 | lung | 1 | Misharin - Unpublished | Unpublished | Ingest source study. | Misharin_2021 | INGEST | TODO | 2024-09-30T23:59:59.999Z | 2024-05-30T19:26:13.588Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
22 | Kidney v1.0 | kidney | 1 | Krebs (2020) Science Immunology | 10.1126/sciimmunol.aba4163 | Ingest source study. | Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:49.201Z | 2024-05-20T07:03:49.283Z | dc0b65b0-7713-46f0-a339-0b03ea786046 | #1034 | 1 | https://doi.org/10.1126/sciimmunol.aba4163 | https://contribute.data.humancellatlas.org/projects/detail?uuid=dc0b65b0-7713-46f0-a339-0b03ea786046&tab=data | Published in DCP | wrangled | PathogenInducedResidentMemory | FALSE | raw not available/ on reasonable request | A mixture of open and managed | Data available upon reasonable request from contributors | 081122: Added for Kidney Atlas. Cell counts in supplementary link. Other data available upon reasonable request from contributors | https://explore.data.humancellatlas.org/projects/dc0b65b0-7713-46f0-a339-0b03ea786046/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23 | Gut v1.0 | gut | 1 | Tatiana Karakasheva, karakashet@chop.edu - Unpublished | Unpublished | Ingest source study. | hamilton_priv | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-20T07:03:43.986Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
24 | Kidney v1.0 | kidney | 1 | Zhang (2021) Proceedings of the National Academy of Sciences | 10.1073/pnas.2103240118 | Ingest source study. | Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:49.681Z | 2024-05-20T07:03:49.685Z | 7c599029-7a3c-4b5c-8e79-e72c9a9a65fe | #1036 | 1 | https://doi.org/10.1073/pnas.2103240118 | https://contribute.data.humancellatlas.org/projects/detail?uuid=7c599029-7a3c-4b5c-8e79-e72c9a9a65fe&tab=data | Published in DCP | wrangled | RenalTumorMicroenvironment | FALSE | raw not available/ will be uploaded to dbGAP | GSE159115; PRJNA667716 | All managed access | De anonimised matrices available in GEO. Rest of data in the publication or available in the future in dbGAP? | 081122: Added for Kidney Atlas. Raw data does not seem available right now. De-anonimised matrices in GEO | https://explore.data.humancellatlas.org/projects/7c599029-7a3c-4b5c-8e79-e72c9a9a65fe/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
25 | Heart v1.0 | heart | 2 | Hill (2022) Nature | 10.1038/s41586-022-04989-3 | Ingest source study. | Integrated multi-omic characterization of congenital heart disease | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:51.704Z | 2024-05-20T07:03:51.707Z | c9e83418-a9f0-4ed1-ab4f-56d9513417bf | #1223 | 1 | https://doi.org/10.1038/s41586-022-04989-3 | https://contribute.data.humancellatlas.org/projects/detail?uuid=c9e83418-a9f0-4ed1-ab4f-56d9513417bf&tab=data | Published in DCP | wrangled | MultiomicCongenitalHeartDisease | TRUE | SRP375872; SRP393509; GSE203273; GSE203274; PRJNA839347; PRJNA842850 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/c9e83418-a9f0-4ed1-ab4f-56d9513417bf/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
26 | Lung v1.0 | lung | 1 | Wang (2020) eLife | 10.7554/elife.62522 | Ingest source study. | Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:44.386Z | 2024-05-20T07:03:44.389Z | 01aacb68-4076-4fd9-9eb9-aba0f48c1b5a | 1 | https://doi.org/10.7554/elife.62522 | https://contribute.data.humancellatlas.org/projects/detail?uuid=01aacb68-4076-4fd9-9eb9-aba0f48c1b5a&tab=data | Published in DCP | wrangled | SARS-CoV2ControlHostGenes | FALSE | raw not available/ will be uploaded to dbGAP | GSE161381; GSE161382; GSE161383; PRJNA677987; PRJNA677986; PRJNA677981 | All managed access | Raw sequencing files has been submitted to LungMap Data Collecting Core and will be submitted to dbGAP Processed data including the full list of peaks are available for download and can be explored using the web portal https://www.lungepigenome.org | https://explore.data.humancellatlas.org/projects/01aacb68-4076-4fd9-9eb9-aba0f48c1b5a/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
27 | Heart v1.0 | heart | 2 | Du (2023) Stem Cell Research & Therapy | 10.1186/s13287-023-03256-0 | Ingest source study. | Single cell and lineage tracing studies reveal the impact of CD34+ cells on myocardial fibrosis during heart failure | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:53.015Z | 2024-05-20T07:03:53.096Z | 86fe0a0c-88b3-4a3e-94a1-6f9feadc401e | #1232 | 1 | https://doi.org/10.1186/s13287-023-03256-0 | https://contribute.data.humancellatlas.org/projects/detail?uuid=86fe0a0c-88b3-4a3e-94a1-6f9feadc401e&tab=data | Published in DCP | wrangled | CD34LineageMyocardialDu | TRUE | SRP415789; SRP364684; GSE222144; GSE198833; PRJNA918371; PRJNA817182 | A mixture of open and managed | Human raw data is managed access and mouse and processed Human data openly available in GEO | 251023: Added as part of Heart Bionetwork List Wait until we know if we should skip mouse data | https://explore.data.humancellatlas.org/projects/86fe0a0c-88b3-4a3e-94a1-6f9feadc401e/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
28 | ORCF v1.0 | oral | 2 | Gareth Thomas, g.thomas@soton.ac.uk - Unpublished | Unpublished | Ingest source study. | Characterisation of human papillomavirus (HPV)-positive (immune hot) and HPV-negative (immune cold) head and neck tumors by single cell RNA sequencing | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-12-06T14:23:05.174Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
29 | Lung v1.0 | lung | 1 | Ordovas-Montanes (2018) Nature | 10.1038/s41586-018-0449-8 | Ingest source study. | Allergic inflammatory memory in human respiratory epithelial progenitor cells | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:42.789Z | 2024-05-20T07:03:42.793Z | 326b36bd-0975-475f-983b-56ddb8f73a4d | #716 | 1 | https://doi.org/10.1038/s41586-018-0449-8 | https://contribute.data.humancellatlas.org/projects/detail?uuid=326b36bd-0975-475f-983b-56ddb8f73a4d&tab=data | Published in DCP | wrangled | AllergicInflammatoryMemory | FALSE | raw managed access phs030434.v1 | phs030434.v1.p1 | A mixture of open and managed | #REF! | https://explore.data.humancellatlas.org/projects/326b36bd-0975-475f-983b-56ddb8f73a4d/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
30 | Skin v1.0 | skin | 2 | Gao (2021) Cell Death & Disease | 10.1038/s41419-021-03724-6 | Ingest source study. | Single cell transcriptional zonation of human psoriasis skin identifies an alternative immunoregulatory axis conducted by skin resident cells | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-28T20:14:44.332Z | 2024-05-28T20:14:44.457Z | 91674dcf-8641-40e6-978d-c1706feffba8 | 1 | https://doi.org/10.1038/s41419-021-03724-6 | https://contribute.data.humancellatlas.org/projects/detail?uuid=91674dcf-8641-40e6-978d-c1706feffba8&tab=data | Published in DCP | wrangled | SkinPsoriasisGao10x | FALSE | raw not available/ will be uploaded to EGA | GSE162183 | A mixture of open and managed | Raw data is managed access at HRA004936 Processed data is open at GSE162183 | Arsenios060923: Part of the Skin Atlas Roadmap List | https://explore.data.humancellatlas.org/projects/91674dcf-8641-40e6-978d-c1706feffba8/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
31 | Lung v1.0 | lung | 1 | Carraro (2021) Nature Medicine | 10.1038/s41591-021-01332-7 | Ingest source study. | Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:44.985Z | 2024-05-20T07:03:44.989Z | e526d91d-cf3a-44cb-80c5-fd7676b55a1d | 1 | https://doi.org/10.1038/s41591-021-01332-7 | https://contribute.data.humancellatlas.org/projects/detail?uuid=e526d91d-cf3a-44cb-80c5-fd7676b55a1d&tab=data | Published in DCP | wrangled | GompertsAirwatCfCells | TRUE | SRP261880; GSE150674; PRJNA633134 | All fully open | Missing cell count | https://explore.data.humancellatlas.org/projects/e526d91d-cf3a-44cb-80c5-fd7676b55a1d/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
32 | Kidney v1.0 | kidney | 1 | McEvoy (2022) Nature Communications | 10.1038/s41467-022-35297-z | Ingest source study. | Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:49.989Z | 2024-05-20T07:03:50.096Z | 77c13c40-a598-4036-807f-be09209ec2dd | #1081 | 1 | https://doi.org/10.1038/s41467-022-35297-z | https://contribute.data.humancellatlas.org/projects/detail?uuid=77c13c40-a598-4036-807f-be09209ec2dd&tab=data | Published in DCP | wrangled | KidneySexBasedTranscriptome | TRUE | SRP373380; GSE202109; PRJNA834732 | All fully open | Imported from nxn db 2023-02-13 | of interest for kidney atlas? | https://explore.data.humancellatlas.org/projects/77c13c40-a598-4036-807f-be09209ec2dd/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
33 | Kidney v1.0 | kidney | 1 | Muto (2021) Nature Communications | 10.1038/s41467-021-22368-w | Ingest source study. | Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:49.489Z | 2024-05-20T07:03:49.581Z | 2af52a13-65cb-4973-b513-39be38f2df3f | 0 | https://doi.org/10.1038/s41467-021-22368-w | https://contribute.data.humancellatlas.org/projects/detail?uuid=2af52a13-65cb-4973-b513-39be38f2df3f&tab=data | lattice | lattice | Singlecelltranscriptionalandchromatinaccessibility | TRUE | lattice | GSE151302; SRP264987; PRJNA635415 | #ERROR! | #ERROR! | #ERROR! | https://explore.data.humancellatlas.org/projects/2af52a13-65cb-4973-b513-39be38f2df3f/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
34 | Retina v1.0, Retina v2.0 | eye | 1, 3 | Voigt (2019) Experimental Eye Research | 10.1016/j.exer.2019.05.001 | Ingest source study. | Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:45.808Z | 2024-05-20T07:03:45.897Z | 4bec484d-ca7a-47b4-8d48-8830e06ad6db | 0 | https://doi.org/10.1016/j.exer.2019.05.001 | https://contribute.data.humancellatlas.org/projects/detail?uuid=4bec484d-ca7a-47b4-8d48-8830e06ad6db&tab=data | Published in DCP | wrangled | HumanFoveaRetinaScheetzSheffield | TRUE | SRP194595; GSE130636; PRJNA540843 | All fully open | #REF! | Retina Foveal vs Peripheral retina; AutoImported Snapshot 2021-06-03 | https://explore.data.humancellatlas.org/projects/4bec484d-ca7a-47b4-8d48-8830e06ad6db/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
35 | MSK v1.0 | musculoskeletal | 3 | Scripture-Adams (2022) Communications Biology | 10.1038/s42003-022-03938-0 | Ingest source study. | Single nuclei transcriptomics of muscle reveals intra-muscular cell dynamics linked to dystrophin loss and rescue | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T07:59:37.084Z | 50048186-1324-44d5-bc54-ed0eebe4ef5c | 0 | https://doi.org/10.1038/s42003-022-03938-0 | https://contribute.data.humancellatlas.org/projects/detail?uuid=50048186-1324-44d5-bc54-ed0eebe4ef5c&tab=data | New | not wrangled | PRJNA772047 | All fully open | #REF! | Part of MSK list | https://explore.data.humancellatlas.org/projects/50048186-1324-44d5-bc54-ed0eebe4ef5c/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
36 | ORCF v1.0 | oral | 2 | Zhu (2023) Archives of Oral Biology | 10.1016/j.archoralbio.2023.105687 | Ingest source study. | Mural cell composition and functional analysis in the healing process of human gingiva from periodontal intrabony defects | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-08-19T13:44:34.407Z | 2025-01-17T04:26:30.811Z | 2433c1e4-5a12-46a5-b2d5-d3554a7694f2 | #1314 | 0 | https://doi.org/10.1016/j.archoralbio.2023.105687 | https://contribute.data.humancellatlas.org/projects/detail?uuid=2433c1e4-5a12-46a5-b2d5-d3554a7694f2&tab=data | Published in DCP | wrangled | MuralGingivaZhu | TRUE | SRP384974; GSE207502; PRJNA855933 | All fully open | #REF! | Part of ORCF list | https://explore.data.humancellatlas.org/projects/2433c1e4-5a12-46a5-b2d5-d3554a7694f2/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
37 | ORCF v1.0 | oral | 2 | King (2021) Science Immunology | 10.1126/sciimmunol.abe6291 | Ingest source study. | Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-08-19T13:53:11.403Z | 2024-08-19T13:53:11.698Z | 24d0dbbc-54eb-4904-8141-934d26f1c936 | #593 | 1 | https://doi.org/10.1126/sciimmunol.abe6291 | https://contribute.data.humancellatlas.org/projects/detail?uuid=24d0dbbc-54eb-4904-8141-934d26f1c936&tab=data | Published in DCP | wrangled | HumanBCellsTonsils | TRUE | E-MTAB-8999; E-MTAB-9003; E-MTAB-9005; PRJEB38087; PRJEB38077 | All fully open | #REF! | E-MTAB-8999 contains bulk data and was not wrangled If rds files have the coordinates this could be wranlged to cellxgene | https://explore.data.humancellatlas.org/projects/24d0dbbc-54eb-4904-8141-934d26f1c936/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
38 | Pancreas v1.0 | pancreas | 2 | Xin (2018) Diabetes | 10.2337/db18-0365 | Ingest source study. | Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response | INGEST | DONE | 2025-06-30T23:59:59.999Z | 2024-05-28T19:57:35.398Z | 2024-05-28T19:57:35.546Z | 27e2e0ae-5971-4927-aac1-19e81804097b | 1 | https://doi.org/10.2337/db18-0365 | https://contribute.data.humancellatlas.org/projects/detail?uuid=27e2e0ae-5971-4927-aac1-19e81804097b&tab=data | Published in DCP | wrangled | pancreasNormalIslets | TRUE | GSE114297 | All fully open | #REF! | Imported from nxn db 2021-10-12; Notes: Primary. Healthy. Files are in BAM format | https://explore.data.humancellatlas.org/projects/27e2e0ae-5971-4927-aac1-19e81804097b/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
39 | Organoid-Endoderm v1.0 | organoid | 3 | Sampaziotis (2021) Science | 10.1126/science.aaz6964 | Ingest source study. | Cholangiocyte organoids can repair bile ducts after transplantation in the human liver | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:09:48.714Z | 6a03e0bc-c818-427c-9917-5d9b0ced7871 | 0 | https://doi.org/10.1126/science.aaz6964 | https://contribute.data.humancellatlas.org/projects/detail?uuid=6a03e0bc-c818-427c-9917-5d9b0ced7871&tab=data | Eligible | not wrangled | E-MTAB-8495 | All fully open | #REF! | organoid data Project found while looking for data from an HCA publication | https://explore.data.humancellatlas.org/projects/6a03e0bc-c818-427c-9917-5d9b0ced7871/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
40 | Skin v1.0 | skin | 2 | Theocharidis (2022) Nature Communications | 10.1038/s41467-021-27801-8 | Ingest source study. | Single cell transcriptomic landscape of diabetic foot ulcers | INGEST | TODO | 2025-06-30T23:59:59.999Z | 2024-05-28T20:15:40.949Z | 8cd1483b-dd6a-4152-a875-c741ba1693c6 | #1184 | 1 | https://doi.org/10.1038/s41467-021-27801-8 | https://contribute.data.humancellatlas.org/projects/detail?uuid=8cd1483b-dd6a-4152-a875-c741ba1693c6&tab=data | Stalled | stalled | EGAS00001005271; GSE165816; GSE166120 | All fully open | Arsenios060923: Part of the Skin Atlas Roadmap List see ebi-ait/hca-ebi-wrangler-central#1184 | https://explore.data.humancellatlas.org/projects/8cd1483b-dd6a-4152-a875-c741ba1693c6/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
41 | Kidney v1.0 | kidney | 1 | Muto (2022) Nature Communications | 10.1038/s41467-022-34255-z | Ingest source study. | Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:50.190Z | 2024-12-20T06:26:08.176Z | 9bef1e81-e5d9-4ece-81cb-ab7449232021 | 0 | https://doi.org/10.1038/s41467-022-34255-z | https://contribute.data.humancellatlas.org/projects/detail?uuid=9bef1e81-e5d9-4ece-81cb-ab7449232021&tab=data | Submitted | wrangled | CellularComplexityADPKD | TRUE | down-prioritized in kidney list | GSE185948 | All fully open | Matrices and seq files in GEO & SRA | Part of Kidney v1.0 | https://explore.data.humancellatlas.org/projects/9bef1e81-e5d9-4ece-81cb-ab7449232021/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
42 | Lung v2.0 | lung | 2 | Watanabe (2022) American Journal of Respiratory Cell and Molecular Biology | 10.1165/rcmb.2021-0555oc | Ingest source study. | Anomalous Epithelial Variations and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-26T17:04:25.696Z | 2024-05-26T17:04:25.916Z | ad04c8e7-9b7d-4cce-b8e9-01e31da10b94 | 1 | https://doi.org/10.1165/rcmb.2021-0555oc | https://contribute.data.humancellatlas.org/projects/detail?uuid=ad04c8e7-9b7d-4cce-b8e9-01e31da10b94&tab=data | Published in DCP | wrangled | SingleCellTranscriptomeCOPD | TRUE | SRP318548; GSE173896; PRJNA727494 | A mixture of open and managed | Previously published in DCP based on GEO submission. Additional Tier 2 metadata to be added under MA. | 061025: Tier 2 to be added and make it MA | https://explore.data.humancellatlas.org/projects/ad04c8e7-9b7d-4cce-b8e9-01e31da10b94/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
43 | Skin v1.0 | skin | 2 | Kim (2020) Nature Medicine | 10.1038/s41591-019-0733-7 | Ingest source study. | Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report | INGEST | DONE | 2025-06-30T23:59:59.999Z | 2024-05-28T20:15:05.675Z | 2025-05-24T06:29:26.160Z | 9d97f01f-9313-416e-9b07-560f048b2350 | 1 | https://doi.org/10.1038/s41591-019-0733-7 | https://contribute.data.humancellatlas.org/projects/detail?uuid=9d97f01f-9313-416e-9b07-560f048b2350&tab=data | Published in DCP | wrangled | HumanSkinBloodHypSensAndNormalKim | TRUE | project soft deleted on dcp13 | SRP201551; GSE132802; PRJNA549083 | All fully open | #REF! | PBMCs, Skin biopsiesHealthy volunteers vs DiH-DRESS patient, pre- and post treatment; AutoImported Snapshot 2021-06-03. #1372 | https://explore.data.humancellatlas.org/projects/9d97f01f-9313-416e-9b07-560f048b2350/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
44 | GDN v1.0, Immune v1.0 | genetic-diversity, immune | 1, 2 | Perez (2022) Science | 10.1126/science.abf1970 | Ingest source study. | Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:47.881Z | 2024-05-20T07:03:47.885Z | 9fc0064b-84ce-40a5-a768-e6eb3d364ee0 | 0 | https://doi.org/10.1126/science.abf1970 | https://contribute.data.humancellatlas.org/projects/detail?uuid=9fc0064b-84ce-40a5-a768-e6eb3d364ee0&tab=data | lattice | lattice | Single-cellRNA-seqrevealscelltype-specificmolecula | TRUE | lattice | GSE137029; GSE174188; PRJNA564301; PRJNA728702; SRP220690; SRP319208; phs002812 | #ERROR! | #ERROR! | #ERROR! | https://explore.data.humancellatlas.org/projects/9fc0064b-84ce-40a5-a768-e6eb3d364ee0/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
45 | Breast v1.0 | breast | 3 | Gray (2022) Developmental Cell | 10.1016/j.devcel.2022.05.003 | Ingest source study. | A human breast atlas integrating single-cell proteomics and transcriptomics | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-06-20T17:26:27.174Z | 2024-06-20T17:26:27.352Z | 9b876d31-0739-4e96-9846-f76e6a427279 | 0 | https://doi.org/10.1016/j.devcel.2022.05.003 | https://contribute.data.humancellatlas.org/projects/detail?uuid=9b876d31-0739-4e96-9846-f76e6a427279&tab=data | Published in DCP | wrangled | breastTranscriptomeAtlas | TRUE | SRP329970; GSE180878; PRJNA749859 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/9b876d31-0739-4e96-9846-f76e6a427279/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
46 | ORCF v1.0 | oral | 2 | Massoni-Badosa (2024) Immunity | 10.1016/j.immuni.2024.01.006 | Ingest source study. | An atlas of cells in the human tonsil | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-08-19T13:49:14.220Z | 2024-09-16T21:57:11.300Z | 0cc58d0b-1734-4e1d-9113-b32e52f75e36 | 2 | https://doi.org/10.1016/j.immuni.2024.01.006 | https://contribute.data.humancellatlas.org/projects/detail?uuid=0cc58d0b-1734-4e1d-9113-b32e52f75e36&tab=data | Published in DCP | wrangled | MassoniBadosaHumanTonsil | TRUE | ERP156759; EGAS00001006375; E-MTAB-13687; PRJEB71973 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/0cc58d0b-1734-4e1d-9113-b32e52f75e36/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
47 | Gut v1.0 | gut | 1 | Kong (2023) Immunity | 10.1016/j.immuni.2023.01.002 | Ingest source study. | The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon | INGEST | DONE | 2024-12-31T23:59:59.999Z | 2024-05-20T07:03:46.306Z | 2024-05-20T07:03:46.311Z | cae461de-ecbd-482f-a5d4-11d607fc12ba | #1087 | 1 | https://doi.org/10.1016/j.immuni.2023.01.002 | https://contribute.data.humancellatlas.org/projects/detail?uuid=cae461de-ecbd-482f-a5d4-11d607fc12ba&tab=data | Published in DCP | wrangled | Landscape-ileum-colon | FALSE | raw managed access DUOS-000146; DUOS-000145 | DUOS-000146 | All managed access | Managed access data in Duos DUOS-000146 CD_Atlas_2021_GIDER; DUOS-000145 CD_Atlas_2021_PRISM | Gut Cell Atlas | https://explore.data.humancellatlas.org/projects/cae461de-ecbd-482f-a5d4-11d607fc12ba/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
48 | Organoid-Neural v1.0 | organoid | 3 | Xiang (2019) Cell Stem Cell | 10.1016/j.stem.2018.12.015 | Ingest source study. | hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T07:44:06.018Z | #N/A | 0 | https://doi.org/10.1016/j.stem.2018.12.015 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
49 | Lung v2.0, ORCF v1.0 | lung, oral | 2 | Ren (2021) Cell | 10.1016/j.cell.2021.01.053 | Ingest source study. | COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-26T17:01:54.499Z | 2024-05-26T17:01:54.726Z | 5f607e50-ba22-4598-b1e9-f3d9d7a35dcc | #953 | 0 | https://doi.org/10.1016/j.cell.2021.01.053 | https://contribute.data.humancellatlas.org/projects/detail?uuid=5f607e50-ba22-4598-b1e9-f3d9d7a35dcc&tab=data | Published in DCP | wrangled | CovidImmuneAtlas | FALSE | raw managed access HRA001149 | GSE158055 | All managed access | #REF! | The GEO records contain only processed data (raw counts in sparse matrix format) as raw data is unavailable due to patient privacy concerns. http://covid19.cancer-pku.cn/#/summary; AutoImported Snapshot 2021-06-03 | https://explore.data.humancellatlas.org/projects/5f607e50-ba22-4598-b1e9-f3d9d7a35dcc/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
50 | Organoid-Endoderm v1.0 | organoid | 3 | Lim (2023) Cell Stem Cell | 10.1016/j.stem.2022.11.013 | Ingest source study. | Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:14:07.838Z | #N/A | 0 | https://doi.org/10.1016/j.stem.2022.11.013 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
51 | Organoid-Endoderm v1.0 | organoid | 3 | Salahudeen (2020) Nature | 10.1038/s41586-020-3014-1 | Ingest source study. | Progenitor identification and SARS-CoV-2 infection in human distal lung organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:16:46.802Z | #N/A | 0 | https://doi.org/10.1038/s41586-020-3014-1 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
52 | Skin v1.0 | skin | 2 | Xu (2021) Nature | 10.1038/s41586-021-04221-8 | Ingest source study. | Anatomically distinct fibroblast subsets determine skin autoimmune patterns | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-28T20:16:05.254Z | 2024-05-28T20:16:05.401Z | 69324a96-a68a-4514-bbb4-f8f3ea4bd0f1 | 1 | https://doi.org/10.1038/s41586-021-04221-8 | https://contribute.data.humancellatlas.org/projects/detail?uuid=69324a96-a68a-4514-bbb4-f8f3ea4bd0f1&tab=data | Published in DCP | wrangled | SkinFibroblastAutoimmuneXu10x | FALSE | raw managed PRJCA006797 | All fully open | Analysis file are archived in https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA006797 | Arsenios070923: Part of the Skin Atlas Roadmap List Analysis files in https://ngdc.cncb.ac.cn/omix/release/OMIX691 | https://explore.data.humancellatlas.org/projects/69324a96-a68a-4514-bbb4-f8f3ea4bd0f1/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
53 | Gut v1.0 | gut | 1 | Agace - Unpublished | Unpublished | Ingest source study. | agace_priv | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-28T21:39:27.934Z | c8503de8-d02d-4bda-ad06-4c851b37fa97 | 0 | FALSE | https://contribute.data.humancellatlas.org/projects/detail?uuid=c8503de8-d02d-4bda-ad06-4c851b37fa97&tab=data | In progress | not wrangled | MA dataset | All managed access | #REF! | Denmark MA submission No5 | https://explore.data.humancellatlas.org/projects/c8503de8-d02d-4bda-ad06-4c851b37fa97/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
54 | Skin v1.0 | skin | 2 | Dunlap (2022) JCI Insight | 10.1172/jci.insight.156341 | Ingest source study. | Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-28T20:14:16.140Z | 2024-05-28T20:14:16.305Z | cbd3d276-9f24-4af9-8381-b11f6cdbdc4b | 1 | https://doi.org/10.1172/jci.insight.156341 | https://contribute.data.humancellatlas.org/projects/detail?uuid=cbd3d276-9f24-4af9-8381-b11f6cdbdc4b&tab=data | Published in DCP | wrangled | InfiltratingTCellsLupus | TRUE | GSE186476 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/cbd3d276-9f24-4af9-8381-b11f6cdbdc4b/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
55 | Heart v1.0 | heart | 2 | Tucker (2020) Circulation | 10.1161/circulationaha.119.045401 | Ingest source study. | Transcriptional and Cellular Diversity of the Human Heart | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:51.317Z | 2024-05-20T07:03:51.381Z | 2184e63d-82d8-4ab2-839e-e93f8395f568 | #1194 | 1 | https://doi.org/10.1161/circulationaha.119.045401 | https://contribute.data.humancellatlas.org/projects/detail?uuid=2184e63d-82d8-4ab2-839e-e93f8395f568&tab=data | Published in DCP | wrangled | HeartDiversityTucker10x | FALSE | raw managed phs001539 | phs001539.v1.p1 | All managed access | #REF! | This is managed access but seems a high value dataset; Also on single cell portal at SCP498; AutoImported Snapshot 2021-06-03 | https://explore.data.humancellatlas.org/projects/2184e63d-82d8-4ab2-839e-e93f8395f568/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
56 | Organoid-Endoderm v1.0 | organoid | 3 | Wesley (2022) Nature Cell Biology | 10.1038/s41556-022-00989-7 | Ingest source study. | Single-cell atlas of human liver development reveals pathways directing hepatic cell fates | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:06:43.835Z | #N/A | 0 | https://doi.org/10.1038/s41556-022-00989-7 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
57 | Development v1.0, Organoid-Endoderm v1.0 | development, organoid | 3 | Yu (2021) Cell | 10.1016/j.cell.2021.04.028 | Ingest source study. | Charting human development using a multi-endodermal organ atlas and organoid models | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-30T17:27:06.967Z | 2024-05-30T17:27:07.103Z | 8ab8726d-81b9-4bd2-acc2-4d50bee786b4 | 0 | https://doi.org/10.1016/j.cell.2021.04.028 | https://contribute.data.humancellatlas.org/projects/detail?uuid=8ab8726d-81b9-4bd2-acc2-4d50bee786b4&tab=data | lattice | lattice | Anorganoidandmulti-organdevelopmentalcellatlasreve | TRUE | lattice | #ERROR! | #ERROR! | #ERROR! | https://explore.data.humancellatlas.org/projects/8ab8726d-81b9-4bd2-acc2-4d50bee786b4/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
58 | GDN v1.0 | genetic-diversity | 2 | Chloe Villani, AVILLANI@mgh.harvard.edu - Unpublished | Unpublished | Ingest source study. | Villani Lab_COVID-19 datasets | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-05-28T19:07:14.974Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
59 | Organoid-Endoderm v1.0 | organoid | 3 | Capeling (2022) Cell Reports | 10.1016/j.celrep.2022.110379 | Ingest source study. | Suspension culture promotes serosal mesothelial development in human intestinal organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T17:27:30.765Z | #N/A | 0 | https://doi.org/10.1016/j.celrep.2022.110379 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
60 | Organoid-Neural v1.0 | organoid | 3 | Andersen (2020) Cell | 10.1016/j.cell.2020.11.017 | Ingest source study. | Generation of Functional Human 3D Cortico-Motor Assembloids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T07:44:26.498Z | #N/A | 0 | https://doi.org/10.1016/j.cell.2020.11.017 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
61 | ORCF v1.0 | oral | 2 | Evgeny Denisov, d_evgeniy@oncology.tomsk.ru - Unpublished | Unpublished | Ingest source study. | Unpublished_tongue cancer | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-08-19T13:50:00.304Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
62 | Lung v1.0 | lung | 1 | Johansen (2022) American Journal of Respiratory and Critical Care Medicine | 10.1164/rccm.202108-1901oc | Ingest source study. | Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing | INGEST | TODO | 2024-09-30T23:59:59.999Z | 2024-05-28T23:02:30.619Z | 2c4647ba-c814-4158-8ea9-6889930e4dfe | #1098 | 1 | https://doi.org/10.1164/rccm.202108-1901oc | https://contribute.data.humancellatlas.org/projects/detail?uuid=2c4647ba-c814-4158-8ea9-6889930e4dfe&tab=data | Stalled | stalled | It's complicated | Not clear where data is | High Priority for Lung Bionetwork with regards to Atlas building. I could not find many of the details including data availability at quick pass. Wranglers to assess Eligibility or access to data. Stalled while waiting for contributors | https://explore.data.humancellatlas.org/projects/2c4647ba-c814-4158-8ea9-6889930e4dfe/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
63 | Lung v2.0 | lung | 2 | Lehmann - Unpublished | Unpublished | Ingest source study. | Lehmann_unpubl | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-06-25T05:52:26.602Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
64 | Lung v2.0 | lung | 2 | Natri (2023) bioRxiv | 10.1101/2023.03.17.533161 | Ingest source study. | Cell type-specific and disease-associated eQTL in the human lung | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-06-25T05:48:13.595Z | 2024-06-25T05:48:13.905Z | 7bc1f14b-5e64-4c7f-86b0-23596b97e2aa | 1 | https://doi.org/10.1101/2023.03.17.533161 | https://contribute.data.humancellatlas.org/projects/detail?uuid=7bc1f14b-5e64-4c7f-86b0-23596b97e2aa&tab=data | Published in DCP | wrangled | eQTL-lung | TRUE | GSE227136; PRJNA945854 | All fully open | #REF! | High Priority Lung project - primary data clarified with help of lung atlas paper | https://explore.data.humancellatlas.org/projects/7bc1f14b-5e64-4c7f-86b0-23596b97e2aa/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
65 | Lung v2.0 | lung | 2 | Nawijn - Unpublished | Unpublished | Ingest source study. | Nawijn_unpubl - Bronchial biopsies from Healthy/Asthma donors | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-06-25T05:51:53.666Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
66 | Pancreas v1.0 | pancreas | 2 | Tosti (2021) Gastroenterology | 10.1053/j.gastro.2020.11.010 | Ingest source study. | Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas | INGEST | DONE | 2025-06-30T23:59:59.999Z | 2024-05-20T07:03:53.708Z | 2024-11-01T20:19:35.849Z | b3938158-4e8d-4fdb-9e13-9e94270dde16 | #1296 | 1 | https://doi.org/10.1053/j.gastro.2020.11.010 | https://contribute.data.humancellatlas.org/projects/detail?uuid=b3938158-4e8d-4fdb-9e13-9e94270dde16&tab=data | Published in DCP | wrangled | PancreasTopographiesTosti10x | FALSE | all managed access deposited in EGA | EGAS00001004653 | All managed access | Analysis files available to download in http://singlecell.charite.de/pancreas | 240724 AC: Changed status to eligible, analysis files (seurat or exprData) are now available for download in the supplementary link http://singlecell.charite.de/pancreas | https://explore.data.humancellatlas.org/projects/b3938158-4e8d-4fdb-9e13-9e94270dde16/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
67 | Organoid-Endoderm v1.0 | organoid | 3 | Chan (2022) Nature Communications | 10.1038/s41467-022-35253-x | Ingest source study. | The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:21:44.484Z | #N/A | 0 | https://doi.org/10.1038/s41467-022-35253-x | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
68 | Lung v2.0 | lung | 2 | Vannan (2023) bioRxiv | 10.1101/2023.12.15.571954 | Ingest source study. | Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-06-25T05:50:43.097Z | d5177ccd-573c-45e4-8cf1-a25a3a9d69d6 | 1 | https://doi.org/10.1101/2023.12.15.571954 | https://contribute.data.humancellatlas.org/projects/detail?uuid=d5177ccd-573c-45e4-8cf1-a25a3a9d69d6&tab=data | Submitted | wrangled | SRP532339; GSE250346; PRJNA1160022 | It's complicated | Raw is mentioned to be open, but might not be public yet | 260224: part of Lung v2 | https://explore.data.humancellatlas.org/projects/d5177ccd-573c-45e4-8cf1-a25a3a9d69d6/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
69 | Organoid-Endoderm v1.0 | organoid | 3 | Han (2020) Nature | 10.1038/s41586-020-2901-9 | Ingest source study. | Identification of SARS-CoV-2 inhibitors using lung and colonic organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T17:28:02.134Z | #N/A | 0 | https://doi.org/10.1038/s41586-020-2901-9 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
70 | Kidney v1.0 | kidney | 1 | Lake (2023) Nature | 10.1038/s41586-023-05769-3 | Ingest source study. | An atlas of healthy and injured cell states and niches in the human kidney | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-03-17T18:45:47.710Z | 72f3aecd-1116-4b01-8df9-d4738050f66c | 0 | https://doi.org/10.1038/s41586-023-05769-3 | https://contribute.data.humancellatlas.org/projects/detail?uuid=72f3aecd-1116-4b01-8df9-d4738050f66c&tab=data | Not eligible | stalled | #N/A | #N/A | partially lattice | #N/A | All fully open | Seems to combine data from different sources, including data from a DCP published "Lattice" dataset. | This Kidney Bionetwork project seems to be a compendium of data from different sources. At least part of it is already in DCP submitted by Lattice. Would require a larger DCP discussion on how to handle these scenarios going forward. See ticket below for m | https://explore.data.humancellatlas.org/projects/72f3aecd-1116-4b01-8df9-d4738050f66c/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
71 | Organoid-Endoderm v1.0 | organoid | 3 | Sarvestani (2021) Nature Communications | 10.1038/s41467-020-20351-5 | Ingest source study. | Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T17:27:50.848Z | #N/A | 0 | https://doi.org/10.1038/s41467-020-20351-5 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
72 | Organoid-Endoderm v1.0 | organoid | 3 | Lamers (2021) The EMBO Journal | 10.15252/embj.2020105912 | Ingest source study. | An organoid‚Äêderived bronchioalveolar model for SARS‚ÄêCoV‚Äê2 infection of human alveolar type II‚Äêlike cells | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:29:38.019Z | #N/A | 0 | https://doi.org/10.15252/embj.2020105912 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
73 | Kidney v1.0 | kidney | 1 | Stewart (2019) Science | 10.1126/science.aat5031 | Ingest source study. | Spatiotemporal immune zonation of the human kidney | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:48.887Z | 2024-05-20T07:03:48.981Z | abe1a013-af7a-45ed-8c26-f3793c24a1f4 | 1 | https://doi.org/10.1126/science.aat5031 | https://contribute.data.humancellatlas.org/projects/detail?uuid=abe1a013-af7a-45ed-8c26-f3793c24a1f4&tab=data | Published in DCP | wrangled | KidneySingleCellAtlas | TRUE | S-SUBS7; ERP120466 | A mixture of open and managed | https://explore.data.humancellatlas.org/projects/abe1a013-af7a-45ed-8c26-f3793c24a1f4/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
74 | MSK v1.0 | musculoskeletal | 3 | De Micheli (2020) Skeletal Muscle | 10.1186/s13395-020-00236-3 | Ingest source study. | A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T08:07:03.048Z | 97fa8470-a17a-4ea0-8c5b-f2e54086f305 | 0 | https://doi.org/10.1186/s13395-020-00236-3 | https://contribute.data.humancellatlas.org/projects/detail?uuid=97fa8470-a17a-4ea0-8c5b-f2e54086f305&tab=data | New | not wrangled | GSE143704 | All fully open | #REF! | Part of MSK | https://explore.data.humancellatlas.org/projects/97fa8470-a17a-4ea0-8c5b-f2e54086f305/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
75 | Skin v1.0 | skin | 2 | Belote (2021) Nature Cell Biology | 10.1038/s41556-021-00740-8 | Ingest source study. | Human melanocyte development and melanoma dedifferentiation at single-cell resolution | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-28T20:12:25.025Z | 2024-05-28T20:12:25.201Z | a4f154f8-5cc9-40b5-b8d7-af90afce8a8f | #853 | 1 | https://doi.org/10.1038/s41556-021-00740-8 | https://contribute.data.humancellatlas.org/projects/detail?uuid=a4f154f8-5cc9-40b5-b8d7-af90afce8a8f&tab=data | Published in DCP | wrangled | HumanMelanocyteDevelopment | TRUE | SRP256176; GSE151091; PRJNA625154 | All fully open | #REF! | Skin cell atlas. Stalled as it's blocked by the Test Data PR. | https://explore.data.humancellatlas.org/projects/a4f154f8-5cc9-40b5-b8d7-af90afce8a8f/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
76 | Organoid-Neural v1.0 | organoid | 3 | Miura (2020) Nature Biotechnology | 10.1038/s41587-020-00763-w | Ingest source study. | Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T07:44:48.261Z | #N/A | 0 | https://doi.org/10.1038/s41587-020-00763-w | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
77 | GDN v1.0 | genetic-diversity | 2 | Kayla Barnes, kbarnes@broadinstitute.org - Unpublished | Unpublished | Ingest source study. | Malawi - longitudinal of infant immunity | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-05-28T19:10:19.513Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
78 | Development v1.0 | development | 3 | Sridhar (2020) Cell Reports | 10.1016/j.celrep.2020.01.007 | Ingest source study. | Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-08-08T13:17:37.805Z | 2025-06-06T10:49:13.204Z | 4bdaedeb-99ae-4fb4-be69-57497cf98b90 | 0 | https://doi.org/10.1016/j.celrep.2020.01.007 | https://contribute.data.humancellatlas.org/projects/detail?uuid=4bdaedeb-99ae-4fb4-be69-57497cf98b90&tab=data | Published in DCP | wrangled | FetalRetinahPSCOrganoidsSridhar | TRUE | GSE142526; SRP238587; PRJNA597325 | All fully open | #REF! | Fetal retina, hPSC-derived retinal organoids, long-term retinal cultures; AutoImported Snapshot 2021-06-03 | https://explore.data.humancellatlas.org/projects/4bdaedeb-99ae-4fb4-be69-57497cf98b90/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
79 | Pancreas v1.0 | pancreas | 2 | Segerstolpe (2016) Cell Metabolism | 10.1016/j.cmet.2016.08.020 | Ingest source study. | Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes | INGEST | DONE | 2025-06-30T23:59:59.999Z | 2024-05-20T07:03:54.206Z | 2024-05-20T07:03:54.209Z | ae71be1d-ddd8-4feb-9bed-24c3ddb6e1ad | 1 | https://doi.org/10.1016/j.cmet.2016.08.020 | https://contribute.data.humancellatlas.org/projects/detail?uuid=ae71be1d-ddd8-4feb-9bed-24c3ddb6e1ad&tab=data | Published in DCP | wrangled | Healthy and type 2 diabetes pancreas | TRUE | ERP017126; E-MTAB-5061; PRJEB15401 | #REF! | #REF! | https://explore.data.humancellatlas.org/projects/ae71be1d-ddd8-4feb-9bed-24c3ddb6e1ad/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
80 | Kidney v1.0 | kidney | 1 | Obradovic (2021) Cell | 10.1016/j.cell.2021.04.038 | Ingest source study. | Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:50.585Z | 2024-05-20T07:03:50.589Z | 95d058bc-9cec-4c88-8d2c-05b4a45bf24f | #994 | 1 | https://doi.org/10.1016/j.cell.2021.04.038 | https://contribute.data.humancellatlas.org/projects/detail?uuid=95d058bc-9cec-4c88-8d2c-05b4a45bf24f&tab=data | Published in DCP | wrangled | Califano-Human-10x3pv2 | FALSE | raw not available | All fully open | #REF! | 081122: Added for Kidney Atlas. Raw and processed data available in Supplementary link. | https://explore.data.humancellatlas.org/projects/95d058bc-9cec-4c88-8d2c-05b4a45bf24f/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
81 | Adipose v1.0 | adipose | 3 | Patti, maryelizabeth.patti@joslin.harvard.edu - Unpublished | Unpublished | Ingest source study. | Patti_unpubl | INGEST | TODO | 2025-03-31T23:59:59.999Z | 2024-05-30T18:29:09.314Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
82 | Gut v1.0, Heart v1.0, Lung v2.0, MSK v1.0, ORCF v1.0 | gut, heart, lung, musculoskeletal, oral | 1, 2, 3 | The Tabula Sapiens Consortium* (2022) Science | 10.1126/science.abl4896 | Ingest source study. | The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans | INGEST | DONE | 2025-03-31T23:59:59.999Z | 2024-05-20T07:03:46.410Z | 2024-05-20T07:03:46.415Z | 10201832-7c73-4033-9b65-3ef13d81656a | 0 | https://doi.org/10.1126/science.abl4896 | https://contribute.data.humancellatlas.org/projects/detail?uuid=10201832-7c73-4033-9b65-3ef13d81656a&tab=data | Published in DCP | wrangled | tabulaSapiens | FALSE | raw not available https://registry.opendata.aws/tabula-sapiens/ requires data transfer agreement | All managed access | https://figshare.com/articles/dataset/Tabula_Sapiens_release_1_0/14267219/3 By accessing these data, you agree not to publish any articles containing analyses of genes, cell types or transcriptomic data on a whole atlas or tissue scale prior to initial pub | 19June24 AC: added peer-reviewed publication | https://explore.data.humancellatlas.org/projects/10201832-7c73-4033-9b65-3ef13d81656a/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
83 | Organoid-Endoderm v1.0 | organoid | 3 | Sung Noh Hong, gisnhong@gmail.com - Unpublished | Unpublished | Ingest source study. | Single cell RNA sequencing for the paired TNF-free and -treated intestinal organoids | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T17:26:11.894Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
84 | Organoid-Endoderm v1.0 | organoid | 3 | He (2022) Cell Stem Cell | 10.1016/j.stem.2022.08.002 | Ingest source study. | Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T17:20:18.042Z | #N/A | 0 | https://doi.org/10.1016/j.stem.2022.08.002 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
85 | Lung v1.0 | lung | 1 | Sasha - Unpublished | Unpublished | Ingest source study. | Sasha_X | INGEST | TODO | 2024-09-30T23:59:59.999Z | 2024-05-28T23:06:08.509Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
86 | Adipose v1.0 | adipose | 3 | Blüher, matthias.bluher@medizin.uni-leipzig.de - Unpublished | Unpublished | Ingest source study. | NonoNankam_unpubl | INGEST | TODO | 2025-03-31T23:59:59.999Z | 2024-05-30T18:11:12.507Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
87 | Lung v2.0 | lung | 2 | Trump (2020) Nature Biotechnology | 10.1038/s41587-020-00796-1 | Ingest source study. | Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19 | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-26T17:02:52.398Z | 2024-05-26T17:02:52.696Z | 769a08d1-b8a4-4f1e-95f7-6071a9827555 | #484 | 1 | https://doi.org/10.1038/s41587-020-00796-1 | https://contribute.data.humancellatlas.org/projects/detail?uuid=769a08d1-b8a4-4f1e-95f7-6071a9827555&tab=data | Published in DCP | wrangled | CovidHypertension | FALSE | raw managed EGAS00001004772 | EGAS00001004772 | All managed access | #REF! | processed data here: https://digital.bihealth.org/ https://figshare.com/articles/dataset/Hypertension_delays_viral_clearance_and_exacerbates_airway_hyperinflammation_in_patients_with_COVID-19/13200278; AutoImported Snapshot 2021-06-03 | https://explore.data.humancellatlas.org/projects/769a08d1-b8a4-4f1e-95f7-6071a9827555/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
88 | ORCF v1.0 | oral | 2 | Emanuel Rognoni, e.rognoni@qmul.ac.uk - Unpublished | Unpublished | Ingest source study. | Unpublished_lichen planus | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2024-08-19T14:00:07.584Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
89 | Gut v2.0 | gut | 3 | Chen (2021) Cell | 10.1016/j.cell.2021.11.031 | Ingest source study. | Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps | INGEST | DONE | 2024-12-31T23:59:59.999Z | 2024-05-20T07:03:46.119Z | 2024-05-20T07:03:46.194Z | 50154d1e-2308-44bf-9608-10c7afaa560b | 0 | https://doi.org/10.1016/j.cell.2021.11.031 | https://contribute.data.humancellatlas.org/projects/detail?uuid=50154d1e-2308-44bf-9608-10c7afaa560b&tab=data | Published in DCP | wrangled | HtanPreCancerAltas | FALSE | raw not available https://data.humantumoratlas.org/explore?selectedFilters=%5B%7B%22group%22%3A%22AtlasName%22%2C%22value%22%3A%22HTAN+Vanderbilt%22%7D%5D requires access from dbGAP | phs002371.v8.p2 | A mixture of open and managed | Added for Gut Atlas. Not clear where the data is and many of the details I've added on the front page might require some attention from whoever takes this up | https://explore.data.humancellatlas.org/projects/50154d1e-2308-44bf-9608-10c7afaa560b/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
90 | MSK v1.0 | musculoskeletal | 3 | Heuston (2025) Communications Biology | 10.1038/s42003-024-07445-2 | Ingest source study. | Optimized methods for scRNA-seq and snRNA-seq of skeletal muscle stored in nucleic acid stabilizing preservative | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T07:59:57.734Z | 5063f61f-8c59-4a49-8d96-b0709db399d1 | 0 | https://doi.org/10.1038/s42003-024-07445-2 | https://contribute.data.humancellatlas.org/projects/detail?uuid=5063f61f-8c59-4a49-8d96-b0709db399d1&tab=data | New | not wrangled | GSE282362 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/5063f61f-8c59-4a49-8d96-b0709db399d1/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
91 | Lung v1.0 | lung | 1 | Liang (2022) Journal of Clinical Investigation | 10.1172/jci157338 | Ingest source study. | The ZIP8/SIRT1 axis regulates alveolar progenitor cell renewal in aging and idiopathic pulmonary fibrosis | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-28T23:04:56.319Z | 2024-05-28T23:04:56.506Z | e456c042-f6b6-4cec-a338-1a8ef80bd779 | 1 | https://doi.org/10.1172/jci157338 | https://contribute.data.humancellatlas.org/projects/detail?uuid=e456c042-f6b6-4cec-a338-1a8ef80bd779&tab=data | Published in DCP | wrangled | Liang_Human_Mouse_IPFlung_10x | TRUE | SRP282483; GSE157997; GSE187027; PRJNA663600 | All managed access | Data availability section can be found in open PMC article | High Priority for the Lung Bionetwork in terms of Atlas building. I could not identify where the data might be on a quick assessment. Wranglers to assess | https://explore.data.humancellatlas.org/projects/e456c042-f6b6-4cec-a338-1a8ef80bd779/project-metadata | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
92 | Skin v1.0 | skin | 2 | Wang (2020) Nature Communications | 10.1038/s41467-020-18075-7 | Ingest source study. | Single cell transcriptomics of human epidermis identifies basal stem cell transition states | INGEST | DONE | 2038-01-19T13:14:07.000Z | 2024-05-28T20:12:02.397Z | 2024-05-28T20:12:02.541Z | 66d7d92a-d6c5-492c-815b-f81c7c93c984 | #855 | 1 | https://doi.org/10.1038/s41467-020-18075-7 | https://contribute.data.humancellatlas.org/projects/detail?uuid=66d7d92a-d6c5-492c-815b-f81c7c93c984&tab=data | Published in DCP | wrangled | HumanNeonatalForeskin | TRUE | SRP253883; GSE147482; PRJNA614956 | All fully open | #REF! | Skin cell atlas | https://explore.data.humancellatlas.org/projects/66d7d92a-d6c5-492c-815b-f81c7c93c984/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
93 | Adipose v1.0 | adipose | 3 | Schmidt, sfs@bmb.sdu.dk - Unpublished | Unpublished | Ingest source study. | Schmidt unpubl | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-17T10:46:25.267Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
94 | MSK v1.0 | musculoskeletal | 3 | Soule (2023) Life Science Alliance | 10.26508/lsa.202201806 | Ingest source study. | A protocol for single nucleus RNA-seq from frozen skeletal muscle | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T08:01:39.458Z | 9545d581-adfe-4621-bece-3a563ad294fd | 0 | https://doi.org/10.26508/lsa.202201806 | https://contribute.data.humancellatlas.org/projects/detail?uuid=9545d581-adfe-4621-bece-3a563ad294fd&tab=data | New | not wrangled | All fully open | raw files not provided, no count matrix shown | https://explore.data.humancellatlas.org/projects/9545d581-adfe-4621-bece-3a563ad294fd/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
95 | Adipose v1.0 | adipose | 3 | Tseng, yu-hua.tseng@joslin.harvard.edu - Unpublished | Unpublished | Ingest source study. | Tseng_unpubl | INGEST | TODO | 2025-03-31T23:59:59.999Z | 2024-05-30T18:08:29.874Z | #N/A | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
96 | Organoid-Endoderm v1.0 | organoid | 3 | Roos (2022) Cell Stem Cell | 10.1016/j.stem.2022.04.011 | Ingest source study. | Human branching cholangiocyte organoids recapitulate functional bile duct formation | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-30T08:10:01.967Z | #N/A | 0 | https://doi.org/10.1016/j.stem.2022.04.011 | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
97 | MSK v1.0 | musculoskeletal | 3 | Varshney (2023) bioRxiv | 10.1101/2023.12.15.571696 | Ingest source study. | Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation | INGEST | TODO | 2038-01-19T13:14:07.000Z | 2025-07-25T07:55:47.401Z | a75235c3-8bdb-4579-8db7-47a888536601 | 0 | https://doi.org/10.1101/2023.12.15.571696 | https://contribute.data.humancellatlas.org/projects/detail?uuid=a75235c3-8bdb-4579-8db7-47a888536601&tab=data | New | not wrangled | phs001048.v2.p1 | All managed access | In the v1 of the pre-print it is mentioned that The raw data is being submitted to dbGaP as an update over an existing repository with other FUSION molecular data phs001048.v2.p1. All data including full summary statistics and code used to run analyses in | Part of MSK. Not clear where count matrix lies. | https://explore.data.humancellatlas.org/projects/a75235c3-8bdb-4579-8db7-47a888536601/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
98 | Lung v1.0 | lung | 1 | Mould (2021) American Journal of Respiratory and Critical Care Medicine | 10.1164/rccm.202005-1989oc | Ingest source study. | Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:42.713Z | 2024-05-20T07:03:42.782Z | 272b7602-66cd-4b02-a86b-2b7c9c51a9ea | 1 | https://doi.org/10.1164/rccm.202005-1989oc | https://contribute.data.humancellatlas.org/projects/detail?uuid=272b7602-66cd-4b02-a86b-2b7c9c51a9ea&tab=data | Published in DCP | wrangled | Mould-Human-10x3pv3 | TRUE | GSE151928 | All fully open | #REF! | https://explore.data.humancellatlas.org/projects/272b7602-66cd-4b02-a86b-2b7c9c51a9ea/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
99 | Lung v1.0 | lung | 1 | Goldfarbmuren (2020) Nature Communications | 10.1038/s41467-020-16239-z | Ingest source study. | Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium | INGEST | DONE | 2024-09-30T23:59:59.999Z | 2024-05-20T07:03:43.108Z | 2024-05-20T07:03:43.111Z | 34c9a62c-a610-4e31-b343-8fb7be676f8c | #892 | 1 | https://doi.org/10.1038/s41467-020-16239-z | https://contribute.data.humancellatlas.org/projects/detail?uuid=34c9a62c-a610-4e31-b343-8fb7be676f8c&tab=data | Published in DCP | wrangled | smokingAirwayEpithelium | TRUE | SRP214324; GSE134174; PRJNA554141 | All fully open | #REF! | Lung bionetwork - first atlas draft ticket 892 | https://explore.data.humancellatlas.org/projects/34c9a62c-a610-4e31-b343-8fb7be676f8c/project-metadata | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
100 | Liver v1.0 | liver | 2 | Grun - Unpublished | Unpublished | Ingest source study. | Unpublished RNA-seq samples | INGEST | TODO | 2024-12-31T23:59:59.999Z | 2024-05-28T19:28:33.117Z | #N/A | 0 | FALSE | FALSE | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | #N/A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||