GSE164690 - CellInteractionsHNSCC

[idazucchi]

Project short name:

CellInteractionsHNSCC

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing

• Accessioned data: GSE164690

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]

Smoking metadata is just Y/N with no context. The options for recording it could be:

1. use yes-> active; no-> never
2. skip this piece of metadata
3. ask from contributor, although it's most likely that they won't know and wouldn't reach out to patients after all

I want to go with 2 because I don't want to create wrong data. If we get this metadata with tier 2 collection we will amend the dataset.