CD8ActivationCOPDVillasenor

[arschat]

Project short name:

CD8ActivationCOPDVillasenor

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder
• manuscript

Published study links

• Paper: 10.1164/rccm.202305-0924OC
• Ingest: e870ab56-3537-4b6d-a66f-534fbf8cc57f
• Accessioned data: zenodo RDS

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]

hca-util uuid: abbe2f53-a8b5-4cd7-9826-0012d5d91542

• bmi & age is average per cohort
• it is implied that non-COPD donors had cancer

  discarded lung tissue were obtained from more than 2 cm away from the tumor margin

• sequencing protocol is not described, but references another publication. I used the sequencer that they used for lung tissue (Illumina Nextseq 500)

[arschat]

graph valid & ready for sec review

[anu-shiva]

Project contributors: You could assign yourself as curator :)
(#25 #26 are marked as principal investigator- I could not see this info. I see three people are supervisors though)

Project-funders This mentions another grant (American Heart Association grant 867587)

Dissociation protocol:

• The original paper used for referencing collection protocol mentions protocol for multiple tissues- Synovial tissues, lung tissues and salivary. It looks like you have added the information for the synovial tissues cell isolation. Should this be replaced by the lung tissue dissociation ("Lung tissues were cryopreserved on site, .."). This also has cell size enrichment.
• the 'Collagenase A + DNAse' protocol name may need correction too.

Cell Suspension
Can Supplementary info on Donor_cells go into the ESTIMATED CELL COUNT?

Analysis protocol:
For DERIVATION PROCESS- some info can be added from the Supplementary material- cell filtering, doublet removal?

Analysis file: The file has a checksum provided at https://zenodo.org/records/8393742

[arschat]

Hi Anu! Thanks for the review! I think that the Donor_cells tab in the supplementary table, describes the number of cells in the final matrix that has been sequenced after filtering and QC, while the cell_suspension.estimated_cell_count field describes an estimate of the number of cells loaded in the suspension before the sequencing.

I included all other comments in the submission (thanks for catching out the wrong dissociation protocol!)

• graph valid
• export
• import form sent