phs001457.v1.p1 - TubularCellLupusNephritis

[ofanobilbao]

Project short name:

TubularCellLupusNephritis

Primary Wrangler:

Ida

Secondary Wrangler:

@Wkt8

Link to Ingest

https://contribute.data.humancellatlas.org/projects/detail?uuid=97fca723-d9e9-4263-9f67-335416086f47&tab=project

Associated files

• Google Drive: folder

Published study links

• Paper: Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways
• Accessioned data: phs001457.v1.p1
• Analysis files Immport

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
• [ ] 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

[idazucchi]

The paper and the metadata table mentions 8 blood samples, but there are no cell counts available for them so I've excluded them from the dataset

[idazucchi]

this is a large dataset and the graph validation is failing --> ops ticket

[idazucchi]

passed graph validation locally, still need to update the status in ingest but it's ready for secondary review!

[Wkt8]

Secondary Review: Donor_Organism: Donors with Ethnicity.Text = Black have Ontology ID and Ontology Label empty. We should add Ethnicity Ontology ID and Ethnicity Ontology Label Ontology ID for African-American from HANCESTRO

Good job!

[idazucchi]

I've edited the spreadsheet but the dataset is stuck in graph validating and I can't update the project I ned dev help to:

1. put the project back to metadata valid
2. put the projet to graph valid once I've done the update - the project gets stuck due to its size but passed graph validation locally

[idazucchi]

I've added the missing ontology terms This needs to be moved to graph valid by a dev since the graph validation gets stuck in ingest

Something weird with the biomaterials: submission: 19293 spreadsheet: 19293 api: 19293 project, metadata tab: 19317

I'd like to make sure there are no extra biomaterials in the submission before we export

[idazucchi]

I've followed Amnon's suggestion: I deleted the submission and re-uploaded the spreadsheet

[idazucchi]

Project is graph valid - currently waiting for ebi-ait/dcp-ingest-central#926 to be in production before trying to export This project has ~19.000 biomaterials and ~19.000 links so it will likely fail spreadsheet generation due to the large linkingMap

[idazucchi]

Exporting for R27

[arschat]

Check if exported @Wkt8

[Wkt8]

Did not export - needs re-exporting

[idazucchi]

I've hit export ~11.30am but no files have been exported, are the export jobs stuck in a queue? did the export fail for other reasons?

[ofanobilbao]

Amnon still has not found the cause. He will detach investigation from the release and this dataset. Export seems fine in his local computer. @amnonkhen to export it and let @idazucchi know when it's ready to submit import form

[gabsie]

This dataset is still problematic and is at the end of the queue.

[idazucchi]

Tried to export again at the end of R29 but the export got stuck again