GSE183684 - CREDiseaseRetina

[idazucchi]

Project short name:

CREDiseaseRetina

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Associated files

• Google Drive: folder

Published study links

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

• Accessioned data: GSE183684

• Ingest

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [ ] Upload sheet to validate metadata
• [ ] Transfer raw files to ingest to validate data files
• [ ] Check linking using ingest graph validator
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Submit dataset to Production
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

Donors there's 10 donors + 2 for hiPSC cell lines - Donor 2 was used as starting point for all the organoids --> 12 donors

The human induced pluripotent stem cell (hiPSC) lines (designated as cell line 1 and cell line 2) were derived from peripheral blood mononuclear cells from two separate, unaffected patients: one male donor, 61 years old; and one female donor, 58 years old. The male donor line was designated as cell line 1, and the female line was designated as cell line 2.

post-mortem interval --> I'm assuming it's in hours but I'm not sure

[idazucchi]

the hca-util area is ready but I can't validate the files due to the issue with hca-util sync so it's ready for secondary review

[idazucchi]

Amnon fixed the sync issues so I'm getting to graph valid before secondary review

[arschat]

Very well done, Ida! Nice work figuring out the organoids and cell lines experimental graph. Only a few comments here.

Cell suspension

• Should the cell_suspensions inherit the genotype of the KO organoids?

  Analysis protocol

• The analysis_protocol.alignment_software for the ATAC version is Cellranger-atac. Cellranger is a different software than Cellranger-atac.

Another minor comment I wanted to make is that the input for cell_suspension is in the input specimen column for all the CS, although some are from organoids and some from cell_lines. Similarly, in organoids tab, the input in input specimen column but the cell_lines are listed there. However, it does not break graph validator and ingest seems to detect the correct linking, and fix it (the downloaded spreadsheet is showing different input biomaterials).

[idazucchi]

Hi - thanks for catching the linking issue with the different biomaterials, I'm suprised ingest didn't throw an error for this one

for the genotype I think it makes sense to keep the info because they're still the same cells and have the same genotype I've updated the alignment software and I'm exporting

[idazucchi]

minor update needed to add correspondent

filled import form

[idazucchi]

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