GSE174691 - AlteredSignalingHCM

[idazucchi]

Project short name:

AlteredSignalingHCM

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Altered intercellular communication and extracellular matrix signaling as a potential disease mechanism in human hypertrophic cardiomyopathy

• Accessioned data:

  • GSE161921 healthy --> previously published from the same lab, we should wranlge separately
  • GSE174691 disease

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]

Missing linking information

there is a very extensive donor metadata table in the supplementary materials, and minimal donor metadata in the GEO accession. Unfortunately the donor ids between the two don't match and the metadata available is not sufficient to match them up. In fact there are 2 donors that have the same sex and age so they can't be told apart and the metadata is different for another 4 donors.

43male 44Male 55female 55Male 54female 63Female 73female 74Female

This is stalled until we are allowed to contact the authors and ask for help