GSE222144 - CD34LineageMyocardialDu

[arschat]

Project short name:

CD34LineageMyocardialDu Li-Human-10x3pv3

Primary Wrangler:

Arsenios

Secondary Wrangler:

Ida

Associated files

• Google Drive: folder
• ingest 86fe0a0c-88b3-4a3e-94a1-6f9feadc401e

Published study links

• Paper: Single cell and lineage tracing studies reveal the impact of CD34⁺ cells on myocardial fibrosis during heart failure.

• Accessioned data: GSE222144 (human) GSE198833 (mice) HRA002066 (human heart failure) HRA001765 (human control & inschemic)

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

[arschat]

Will wrangle later when we know for sure if we should wrangle mouse data too for the bionetworks projects.

Human spreadsheet is semi-filled in google drive folder and analysis files have been uploaded in the hca-util upload area with uuid 934bfc59-a634-473c-baa8-f5e87e00b83f.

[arschat]

Notes

Many metadata especially about mice are described in the results, instead of the methods.

Human

• Only the control donor was used from HRA001765. In GSA we could see that both donors are male.
• no specific type of hypertension is mentioned, therefore I added essential hypertension from mondo
• sequencing protocol and analysis protocol for both are identical for two organisms besides the cellranger mkfastq version (human v5, mouse v3.1.0) according to GEO protocol description
• Although human raw fastqs are in GSA, there are also in SRA, therefore isn't these considered public? I have added the human seq files.
• Genome version for human is (accidentally?) stated as mm10. This would not be valid, and since it is stated that standard procedure was used, the default for human data from cellranger v4 is GRCh38

  Mouse

• 3 x 2 mice groups, with 6 pooled donor samples per group/library + 1 standalone bmt mouse
  • TAC 0, tamoxifen at C57BL/6;B6.Cg-Gt(ROSA)26Sortm9(CAG−tdTomato)Hze/J
  • TAC 0, no tamoxifen at C57BL/6
  • TAC 4, tamoxifen at C57BL/6;B6.Cg-Gt(ROSA)26Sortm9(CAG−tdTomato)Hze/J
  • TAC 4, tamoxifen at C57BL/6;B6.Cg-Gt(ROSA)26Sortm9(CAG−tdTomato)Hze/J chimeric Bone marrow transplant mouse
  • TAC 4, no tamoxifen at C57BL/6
  • TAC 12, tamoxifen at C57BL/6;B6.Cg-Gt(ROSA)26Sortm9(CAG−tdTomato)Hze/J
  • TAC 12, no tamoxifen at C57BL/6
• male 8-10 is mentioned here

  Single nucleated live cells were isolated from hearts of 8–10-week-old male mice

• TAC surgery is a model for cardiac hypertrophy. The most appropriate term I found was hypertrophic cardiomyopathy in mondo.

[arschat]

graph valid & ready for sec review

[idazucchi]

good job on this very confusing dataset!

project

• the description is formatted in a weird way, can you add a space for the section names?

donor

• all mice are described in GEO as Cd34-CreERT2;R26-tdTomato
• for the human HF I'd use hypertensive disorder MONDO:0005044 which is more generic

enrichment

Single nucleated live cells were isolated from hearts of 8–10-week-old male mice, 4 and 12 weeks after TAC operation, by enzymatic digestion and sorting the cardiac non-cardiomyocyte cells, further processed for scRNA-seq using the 10 × genomics chromium platform

• no need for red blood cell lysis (has no description)
• based on that bit of the paper and the cell type field in GEO I think you could add the enrichment protocols for CD34+ cells and for non-cardiomyocytes

sequencing

• missing descriptions

analysis file

• count matrix is enough for the content type

[arschat]

Thanks a lot for the comments and the discussion Ida. I model it in another way, there are 25 (6+6+6+1) and some specimens are enriched for cd34 with MACS.

I added all comments

• [X] submitted
• [x] graph valid
• [x] exported
• [x] import form sent

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