E-MTAB-11509 - Burja_10x_SkinBiopsies

anu-shiva commented 1 year ago

Burja_10x_SkinBiopsies

Ida

[x] Convert published metadata to HCA spreadsheet
[x] Manually curate dataset to meet HCA metadata standard
[x] 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
[x] Upload sheet to validate metadata
[x] Transfer raw files to ingest to validate data files
[x] 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 commented 1 year ago

Hello :) The dataset looks good, nice job! I just have a couple comments

fill in the organ part with forearm, leg or breast skin
having now read the whole paper and seeing the AE accession I think that the SSc samples are actually disease samples, although maybe they didn't sample the most severely affected sites - you can add non-fibrotic to gross description

Our cultured skin explants were derived from patients with SSc as a prototype of fibrotic skin pathology.

same id for mechanical and enzymatic! only one of them will be picked up in ingest

for the cultured samples you can fill in the growth medium, culture environment, feeder layer type and timecourse

if you want to fill out library preparation id I'd keep it the same as in AE, without _p

idazucchi commented 1 year ago

the ontology for organ part needs an update breast --> skin of breast forelimb zeugopod --> skin of forearm leg --> skin of leg

and the institute has the ; issue

idazucchi commented 11 months ago

updated and submitted form

ebi-ait / hca-ebi-wrangler-central