GSE165839 - HeartCellsGeneRegulation

[idazucchi]

Project short name:

HeartCellsGeneRegulation

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Associated files

• Google Drive: folder

Published study links

• Paper: Cardiac cell type-specific gene regulatory programs and disease risk association

• Accessioned data: GSE165839 superseries

  • GSE165837 snATAC-seq
  • GSE165838 snRNA-seq

• UCSC cell browser? no accession

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]

useful sample breakdown in the first figure's description donor metadata in supplementary table 1 - in pdf page 16

[idazucchi]

ready for secondary review

[arschat]

Hi Ida! Well done wrangling that project so quickly! I noticed only a couple of happy accidents.

Project - Contributors

• project.contributors.laboratory for some contributors there is a tab character separator and duplication of information
• Nice catch for filling all the provided orcid!

Project - Funders

• project.funders.grant_id There are two grant_ids collapsed in one

Donor organism

• donor_organism.death.cold_perfused could be filled

  Donated hearts were perfused with cold cardioplegia before cardiectomy and then explanted immediately into an ice-cold physiologic solution as we previously described

Specimen & Cell suspension

• Typo in the _.biomaterial_core.biomaterial_description specimen/CS form -> specimen/CS from

Library prep

• In the ATAC_library_prep the library_preparation_protocol.nucleic_acid_source is set to 'bulk nuclei' although it should be 'single nucleus'

Analysis protocol

• You could include a 'raw matrix generation' protocol type, either to a new protocol or add it to a processed matrix generation existing one to describe that the creation of the raw count matrix (both for RNA & ATAC).

[idazucchi]

thanks for reviewing! I applied the suggestions, exported and filled in the import from

[idazucchi]

reviewed in the browser