GSE199850 - Intrarenal Single-Cell Sequencing of Hepatitis B Virus Associated Membranous Nephropathy

[ofanobilbao]

GSE199850 - Intrarenal Single-Cell Sequencing of Hepatitis B Virus Associated Membranous Nephropathy

Project short name:

Xiao-Human-RNAscope

Primary Wrangler:

Wei

Secondary Wrangler:

Ida

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=5f44a860-d96e-4a99-b67e-24e1b8ccfd26

Associated files

• Google Drive: https://drive.google.com/drive/folders/1BShYRxDZvG4MpVB7jt6Mz9hHDZ7C5OHQ

Published study links

• Paper: https://www.frontiersin.org/articles/10.3389/fmed.2022.869284/full#h7

• Accessioned data: GSE199850

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] 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

[Wkt8]

1 Hep B patient and 2 healthy controls in paper, but only the Hep B patient sequencing files and analysis files are available. Have emailed asking if the healthy control data / metadata is available.

[Wkt8]

Emailed again.

[idazucchi]

Hello! I'm done with the secondary review, I have some very small comments, otherwise it looks good!

Project

• you can split the author information into institute and address
• there is no funding information

Donor

• you can remove the age from the description, it makes it easier to address possible future k-anonimity issues

Specimen

• I thought we only used the experiment field for the sequence file tab?
• same k-anonimity issue

Enrichment

• you can add the cell size selected

Cell suspension

• do you want to add the INSDC sample accession?
• the estimated cell count should have the estimated cells in the CS, not the sequenced cells

Analysis

• you could fill out the computational methods

Analysis file

• the genome version is missing in the spreadsheet

[Wkt8]

In Submitted. Still need to fill out the import form.

[Wkt8]

Import form filled out.