GSE145927 - ChimerismKidneyTransplantReject

[ofanobilbao]

Project short name:

ChimerismKidneyTransplantReject

Primary Wrangler:

Ida

Secondary Wrangler:

@arschat

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=4ef86852-aca0-4a91-8522-9968e0e54dbe&tab=project

Associated files

• Google Drive: folder

Published study links

• Paper: Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant

• Accessioned data: GSE145927

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
• [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
• [x] Submit dataset to Production
• [x] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

Donors missing metadata on the donor pre/post treatment for ABMR (antibodies mediated rejection) metadata for other donors --> page 13 supplemental information

Missing metadata

• [ ] is it 3' or 5' ? which version?
• [ ] is vdj data available?
• [ ] sequencing done w/ NovaSeq or HiSeq?
• [ ] mystery donor metadata
• [ ] genome version

[idazucchi]

I've sent an email to the authors to get the missing information - in the meanwhile I validated the dataset and it's ready for secondary review

I will update with the correct information as soon as the authors reply

[arschat]

Hi Ida! Here are my comments from the reviewing.

Project - Funders

• GRAND ID UL1TR002345 is also written UL1 TR002345 with a space.

  Specimen From Organism

• donor numbering in SPECIMEN FROM ORGANISM NAME is sequential but there is mismatch with INPUT DONOR ORGANISM ID field

  Sequence Files

• LIBRARY PREPARATION PROTOCOL ID is the other way round in the GEO (biopsy 1-5 should have 10x_5', biopsy 6-7 should have 10x_3')

[idazucchi]

I've applied the suggestions and graph validated, but I still need some information from the authors. I will ping them again today

[idazucchi]

I will ping the authors again but if they don't reply can we publish the project without the genome version?

[idazucchi]

Project exported correctly, I checked the google bucket

• [x] fill import form

[idazucchi]

checking in the Data portal - one speciment has still has unspecified disease --> normal?

[idazucchi]

ok for this to be released --> will update to add:

• [x] specimen time course for sampling
• [x] add PRJ
• [x] add disease for specimen 7

[idazucchi]

do we want a new term for transplant rejection?

[ofanobilbao]

Only to do the update if capacity allows

[idazucchi]

updated, exported metadata and filled out import form

[idazucchi]

verified in the browser

[idazucchi]

• the cell barcode lenght is wrong for 10x v2

[idazucchi]

updated and filled import form

[idazucchi]

verified in the browser