phs001539 - ChaffinHypertrophicCardiomyopathy

ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.

https://ebi-ait.github.io/hca-ebi-wrangler-central/

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phs001539 - ChaffinHypertrophicCardiomyopathy #1207

Closed idazucchi closed 7 months ago

idazucchi commented 11 months ago

Project short name:

ChaffinHypertrophicCardiomyopathy

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

Google Drive: folder

Published study links

Paper: Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
Accessioned data:
- phs001539
- SCP1303

Ingest

Key Events

[ ] Convert published metadata to HCA spreadsheet
[ ] Manually curate dataset to meet HCA metadata standard
[ ] 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
[ ] 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 commented 10 months ago

Cell suspension: I've exclueded the libraries that didn't pass QC because they are not in the count matrix files Supplementary file: I'm not sure if I should include this or not as a supplementary. It's nice to have information but it's not essential

idazucchi commented 10 months ago

ready for secondary review

arschat commented 10 months ago

Hi, Ida! Excellent wrangling. Only some very minor comments/ suggestions:

Donor

Since organ donor is on Tier 1 metadata, you could include the information that NF donors were organ donors with no history of heart failure in the biomaterial description (maybe donor_organism.death.organ_donation_death_type would be Donation after brainstem death (DBD) since the other option is circulatory death and there was no heart failure although that is not clearly stated in the manuscript)

Analysis protocol

you could add the analysis_protocol.alignment_software CellRanger & analysis_protocol.alignment_software_version 4.0.0

Trimmed reads were aligned to the GRCh38 pre-mRNA human reference (v2020-A) using CellRanger 4.0.0 (cellranger count) with --expect-cells 5000. All other parameters were left as defaults.

Analysis file

you could add the analysis_file.matrix_cell_count for the matrix analysis files

idazucchi commented 10 months ago

thanks for the comments! I've applied your suggestions a part for the death type which we can't infer Exported and filled import form

idazucchi commented 7 months ago

verified in browser