GSE165816 - SkinDiabeticUlcers

[idazucchi]

Project short name:

SkinDiabeticUlcers

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Single cell transcriptomic landscape of diabetic foot ulcers

• Accessioned data:

  • GSE165816 10x
  • GSE166120 NanoString - imaging technique / not eligible? I'm checking the skin paper

Ingest

Key Events

• [x] Convert published metadata to HCA spreadsheet
• [x] Manually curate dataset to meet HCA metadata standard
• [x] 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]

need to confirm with authors:

• [ ] which samples are 10x 3' v2 and which are v3
• [ ] other than foot ulcer samples all remaining samples are healthy skin?

email thread here

[idazucchi]

confirmed that all foor skin samples are either ulcer or healthy, now checking forearm samples

[idazucchi]

Still part of the skin atlas list, waiting for bionetwork lead to start communications again