GSE136831 - COPDalveolarNiche

[idazucchi]

Project short name:

COPDalveolarNiche

Primary Wrangler:

Enrique

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

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

• Accessioned data:

  • GSE136831 - scRNA-seq patients
  • GSE168299 - scRNA-seq mouse
  • GSE47460 - microarray from total RNA

• Ingest project

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]

I'm not sure which accession the network is interested in. My guess would be GSE136831 - scRNA-seq patients but the original paper for this data is actually Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

The re-analysis paper uses a subset of the accession too.

I've emailed Ciro (lung bionetowork) and I'm waiting for a reply

[ESapenaVentura]

This is just a re-analysis of https://data.humancellatlas.org/explore/projects/c16a754f-5da3-46ed-8c1e-6426af2ef625

We should focus on the other ticket if they want the mouse data

[ofanobilbao]

Linking the two tickets here not to forget they both reference one single entry in the Lung Bionetwork tab (Rosas_Kaminsky 2022). #1084

[arschat]

Based on the change in the lung v2 list (Rosas_Kaminski_2022 has been substituted by Kaminski_2020) it look like only human data is required. @idazucchi to confirm with CIro and check if the fastq files exist in the DCP

[idazucchi]

lungPopulationsIPF was publisehd in the DCP in April 2022, while fastq files from GSE136831 only became public on 2022-10-03 so they are not in DCP. I'm checking with CIro if they need both analysis and sequence files, but regardless of that I think we should update the project and add sequence files

reopening the old ticket for lungPopulationsIPF ?

[ofanobilbao]

@gabsie to reach out the lung integration contact. We can close the ticket. @ESapenaVentura to reference the zenhub ticket in Ingest and mark as stalled.