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.

[arschat]

Perfect wrangling Ida! Only a singular comment for donor description:

• in table 1 there is a footnote for T/ N/ M stage of donors 5 & 8 †Pathologically staged. In our description only the † icon is added, however there is no description of what that means. We could either remove the icon and skip the extra info, or add the Pathologically staged in the description of those fields.

[idazucchi]

fixed, exported and filled the form