GSE138262 - WehrensHypertrophicCELSeq2

[arschat]

Project short name:

WehrensHypertrophicCELSeq2 (VanRooij-Human-CELseq2)

Primary Wrangler:

Arsenios

Secondary Wrangler:

Wei

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy
• DOI: 10.1016/j.celrep.2022.110809
• Accessioned data: GSE138262
• ingest: 10a845f7-0361-46fa-92a3-2a36483136b1

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
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [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

[arschat]

Publication uses data from other publications

• Wang et al., 2020 not wrangled: GSE121893 & GSE109816
• Litviňuková et al., 2020 published in DCP: ERP123138

but neither sequence files and analysis files do not include this information.

I will not consider the healthy data, and just wrangle the 5 Hypertrophic cardiomyopathy donors.

[arschat]

Moved files to hca-util upload area and removed from hca-ncbi-cloud-data bucket. hca-util-upload-area uuid: c7512d6d-0c1f-4f63-b664-eb43a6205014

[arschat]

Graph valid & ready for sec review

[Wkt8]

Assigning self for secondary review

[Wkt8]

Hey Arsenios! Looks really good, agree with your choice for only wrangling the HCM donors. The paper laid out a lot of information and I think you modelled it really well.

The only points I have are on the analysis_protocol tab and one point on the project tab:

1. The analysis protocol for barcode_matrix_generation isn't being used in any of the processes.
2. The description for the analysis protocol 'transcript_matrix_generation' feels like it could be fleshed out a bit more, but I'll leave it to your discretion.
3. One point on the project tab: leaving 'the Netherlands' with the 'the' lower-case stylistically doesn't feel right to me. Would change it to 'The Netherlands'

[arschat]

Hi Wei, thanks for the comments! Fix those, exported, and import form sent!

[arschat]

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