GSE151671 - SuryawanshiKidneyAllografts

[ofanobilbao]

Project short name:

SuryawanshiKidneyAllografts

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=6e522b93-9b70-4f0c-9990-b9cff721251b&tab=project

Associated files

• Google Drive: foldr

Published study links

• Paper: Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts

• Accessioned data: GSE151671

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

[idazucchi]

preparing the fastq files 16c73b63-f679-4f67-9d54-117f588171da

[idazucchi]

Donor/Specimens there are two kidney transplant receivers that donated part of their transplant kidney (biopsies) I'm not sure if I captured the disease status correctly for the specimen, I tried to capture the health status at the time of the biopsy. (see the result section of the paper)

[arschat]

Great submission! I found only two minor comments.

Analysis Protocol

Protocol ID matrix generation has spaces

Analysis File

Matrix cell count has 6001 cells, but matrix contains 6000 cells (first column is gene names)

[ofanobilbao]

@gabsie why is this in the stalled column? It is public in DCP already

[gabsie]

something has happened here which I have no explanation for :), I wouldn't reopen just like that - no comment as well.

[ofanobilbao]

As per Operations Review meeting today, closing as it does not seem as there was anything wrong with this dataset