GSE157997_The ZIP8/SIRT1 axis regulates alveolar progenitor cell renewal in aging and idiopathic pulmonary fibrosis

[anu-shiva]

Project short name: Jiang_X

Primary Wrangler: @anu-shiva

Secondary Wrangler:

Associated files

• Google Drive

Published study links

• Paper: Jiang_X

• Accessioned data: GSE157997

Ingest

Key Events

• [x] Convert published metadata to HCA spreadsheet
• [x] Manually curate dataset to meet HCA metadata standard
• [x] 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
• [x] Upload sheet to validate metadata
• [x] 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]

Hi Anu! Great job figuring out all the datasets.

Project

• hca_publication information missing, part of HCA Lung Atlas 2.0
• Project information missing will be added automatically from ingest

  Donors

• Known diseases: normal could be added in the day 0 mouse samples since no bleomycin injury was done

  We performed scRNA-Seq of flow-enriched lung epithelial cells from both young and old mice at baseline (uninjured, day 0) as well as days 4 and 14 after bleomycin injury

• Treatment: likewise, in day 0 no bleomycin injury was done

  Specimen

• Known diseases: idiopathic pulmonary fibrosis (IPF) added for human IPF donors, could be added in specimens too

  Cell suspension

• Cell suspension ID: there is a space in ID mice_Zip8_knockout_sample 1_single_cells between sample & number 1
• Selected cell type(s): all CSs have AEC2. Based on the markers in enrichment protocols, I would suggest epithelial cells.

  Enrichment

• Markers: In results, the markers that were used for enrichment_flow_cytometry of human samples are mentioned:

  we performed scRNA-Seq of freshly isolated flow cytometry–enriched epithelial cells (CD31–CD45–EpCAM+) from explanted lungs of patients with IPF and from healthy donors

• Markers: In GEO description, the markers that were used for enrichment_flow_cytometry of mouse samples are mentioned:

  Young and old mice were first injected with bleomycin. At day 0, day 4 and day 14, the lungs were harvested and digested, and Lin-Epcam+ cells were isolated with FACS, single-cell RNA-seq was performed with the FACS-sorted cells.

  Sequence files

• Read Length: could be filled
• INSDC experiment accession: wrong SRX accession mapping to SRR for row 697, 698, 699, 700, 701. Based on the SRRs should be mapped to SRX12907305, but has an ascending number (SRX129073-06,07,08,09,10).

  Analysis files

• Genome version: All files are mapped to GRCh38. Count matrices of mouse data were aligned to GRCm38 (mm10), and for cell barcode & feature table Genome Version is Not applicable

[idazucchi]

Anu is waiting to export this as a demo with Alex and Dipayan next week