GSE168299 - Sauler-Human-10x3pv2

[arschat]

Project short name: Sauler-Human-10x3pv2

Part of Lung v2.0 atlas

Primary Wrangler:

Arsenios Chatzigeorgiou

Secondary Wrangler:

Associated files

• Google Drive:

Published study links

• Paper: Characterization of the COPD alveolar niche using single-cell RNA sequencing

• Accessioned data: GSE168299

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]

Paper links to 3 different GEO accessions:

1. Previously published human 10x 3' v2 on GSE136831 which is already in DCP
2. Previously published micro-array human data on GSE47460
3. Mouse 10x 3' v3 data on GSE168299 not previously published.

The No. 1 dataset was reanalysed.

Concerning the mouse experiment, all data and metadata needed for wrangling are available. Experimental design is described thoroughly in paper's methods.

Raw & Processed data for GSE168299

• Fastq files in SRA SRX10241392
• Count matrices in Supplementary in GEO GSE168299

Metadata

• Sample name in cell_name & orig.identity in metadata available in GEO.

[anu-shiva]

@idazucchi waiting for answer from contributors

[ofanobilbao]

Seems like the same dataset as https://app.zenhub.com/workspaces/dataset-wrangling-status-5f994cb88e0805001759d2e9/issues/gh/ebi-ait/hca-ebi-wrangler-central/1092. @arschat , @ESapenaVentura , @idazucchi to discuss both

[arschat]

Mouse data are not needed by bionetwork. Closing