PRJNA379992 - Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis

[idazucchi]

Project short name:

Primary Wrangler: @anu-shiva

Secondary Wrangler:

Associated files

• Google Drive: PRJNA379992_Der_LupusNephritis_Hiseq

Published study links

• Paper: Included data Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis

• Accessioned data: PRJNA379992

• 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
• [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
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch witht the authors to request it

[ESapenaVentura]

Need contributor contact:

• Missing analysis
• Some metadata misinformation

[idazucchi]

The dataset is stuck in graph validation - we are waiting on dev fixes

[arschat]

@Wkt8 to help graph validate locally

[anu-shiva]

Graph valid. ready for secondary review

[Wkt8]

Assigning self for secondary review

[Wkt8]

Donor_Organism: Under the 'disease' field, enter 'normal' for the donor_organisms that are marked as healthy instead of leaving them blank

Would be great if we could incorporate the stage of lupus (II/III/IV/V) into the donor_organism description

Collection_Protocol: Not necessary, but I would split up the skin collection and renal collection protocols into two different protocols, and use the ontology term for 'biopsy' (https://ontology.archive.data.humancellatlas.org/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009120) for the skin collection and EFO:0009293 (percutaneous kidney biopsy) for the kidney collection protocol.

Specimen_from_organism There's a specimen for the 'healthy blood' from 'healthy controls' but there is no link to it to a specific organism. I saw that there is a BioSamples accession for the sample Metro_PBMC (SAMN06661569) but there's not really any information attached. Nonetheless, we need to be consistent and have the specimen_from_organism linked to a donor_organism even if the donor_organism has minimal metadata so that the downstream systems are able to parse the data.

I would recommend creating a 'donor_31_Metro_PBMC' donor, and linking the Metro_PBMC specimen to it.

Or alternatively, removing the blood specimen all together as it doesn't seem to be linked to any further cell suspension or sequence file.

Library_preparation I'm a bit confused about the Fluidigm-C1 based library preparation, but we have a row in the assay cheat sheet ( https://docs.google.com/spreadsheets/d/1H9i1BK-VOXtMgGVv8LJZZZ9rbTG4XCQTBRxErdqMvWk/edit#gid=0) which states that it is 'full length' end bias and only generates 1 fastq per cell, which matches up to the sequence_file tab. Maybe change the end bias to match that? Also not sure where you got the information for the cell barcode and umi barcode lengths, please share as I couldn't find it!