GSE195665 - SpatiallyAdultBreastKumar

[idazucchi]

Project short name:

SpatiallyAdultBreastKumar

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: A spatially resolved single-cell genomic atlas of the adult human breast

• Accessioned data: GSE195665

  • GSE234814 visium
  • GSE234817 snRNA-seq
  • GSE235326 scRNA-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]

I've found a few discrepancies in the metadata for visium slides 8-10 and I've relied on the cxg metadata I've also taken metadata or donors 133-1335 from cxg

I need to check withh Dave that we're still using the external portal sheet

[idazucchi]

Finally graph valid!

[arschat]

Project has already been published by lattice. https://explore.data.humancellatlas.org/projects/1ffa2223-28a6-4133-a5a4-badd00faf4bc