GSE224995 - RiskVariantsAF

[idazucchi]

Project short name:

RiskVariantsAF

Primary Wrangler:

Ida

Secondary Wrangler:

Anu

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation

• Accessioned data: GSE224997 superseries

  • GSE224995 snRNA-seq
  • GSE224996 sATAC-seq

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]

the paper doen't explicitly say that the donors are healthy but I think they are, no disease is mentioned and they are not refferred to as patients sample SP-HE-MW200804-C is somewhere also referred to as SP-HE-MW200804-B

[anu-shiva]

Hi Ida, very minor comments, most of these are not absolutely needed, but optional Dissociation protocol: You can add reagents Enrichment protocol: For the size selection- MAX SIZE SELECTED can be added Sequencing protocol :

• The SEQUENCING PROTOCOL NAME is sequencing protocol for both rows- is this unintentional?
• Should NextSeq500 be added too in the IINSTRUMENT MANUFACTURER AND MODEL?

Analysis protocol: typo in Row 7 column B Analysis file: process name and description can be added.

Some descriptions (analysis protocol, library prep have reference numbers still

[idazucchi]

Thanks for reviewing! filled in import form

[idazucchi]

reviewed in browser