GSE202109 - KidneySexBasedTranscriptome

[idazucchi]

Project short name:

KidneySexBasedTranscriptome

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity

• Accessioned data: GSE202109

• Ingest

Key Events

• [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
• [x] 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]

Donors I've sent an email (see thread) to confirm that the donor metadata is correct, there is a mismatch between GEO, UCSC cell browser and the supplementary material Do not export until this is cleared up

Otherwise ready for secondary review, it's graph valid!

[Wkt8]

Apart from the above issue with the mismatch between donor metadata, looks good! Just a couple minor comments -

Dissociation Protocol:

Change description of mechanical_dissociation All living donor samples used for sequencing were processed within one hour of organ retrieval. Briefly, biopsies were collected in RPMI 1640 on ice, and mechanically dissociated with a blade before enzymatic dissociation.

Change description of enzymaticdissociation After mechanical dissociation, specimens were enzymatically digested at 37 °C with 0.1 mg/ml DNase I, 3300 CDA units/ml Collagenase MA and 1430 NP units/ml BP neutral protease for 20 minutes at 37 °C with intermittent agitation in a dissociation protocol optimized to maximize viability and to preserve representation of rare and fragile cell populations_

[idazucchi]

thanks for reviewing! I've applied your suggestions I'm pinging the authors again to confirm the donor metadata before submitting

[idazucchi]

I got the correct donor metadata from the authors, updated the submission and exported the dataset

[gabsie]

@ESapenaVentura to see if the export was successful and then if yes, send import form

[ESapenaVentura]

Done

[idazucchi]

To update:

• missing cell barcode ontology terms