GSE168191 - MultipotentCellRgenerateAlveoli

[idazucchi]

Project short name:

MultipotentCellRgenerateAlveoli

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Human distal airways contain a multipotent secretory cell that can regenerate alveoli

• Accessioned data:

  • GSE168191 - 19 samples COPD+healthy
  • GSE130076 - 1 sample HT280neg_Single cell

ingest

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]

GSE130076

only has one sample but no metadata is available for it so it's impossible to match it up the supplementary table (it could be Donor 7?) - I would rather include minimal metadata for now and amend it later once we get in touch with the contributors

I'm assuming it's a healthy donor since no information is given. I think in this context the distal sample described here is the same as peripheral sample

Cell selection protocol:

For primary human cells, a single-cell suspension was generated as described above and AT2 cells were isolated using the MACS multisort kit, MACs LS columns and the following antibodies: anti-HT2-280 (mouse IgM, Terrace, TB-27AHT2-280, 1:50) and anti-mouse IgM microbeads (Miltenyi, 130-047-302, 1:200).

[idazucchi]

ontology

for distal/peripheral lung I'm using pulmonary alveolar parenchyma
for proximal lung I'm using pulmonary alveolar parenchyma
please feel free to suggest better terms

ready for secondary review!

[arschat]

Hi Ida! Well done wrangling this dataset! I have a few comments here.

Project

• supplementary link, maybe avoid using a URL shortener for clarity reasons, and use "http://ec2-3-236-59-0.compute-1.amazonaws.com:3838/lungmap/" instead

donor

• GSE130076 includes all 6 healthy donors, and leaves only Donor_7 marked as scRNA-seq but not referenced in Fig. 1 like other donors. The GSE130076 donor is has Source name - Distal lung epithelium while it is referenced in the manuscript:

  A new scRNA-seq dataset using only the distal lung epithelium was used to identify a cell-surface marker to isolate primary RAS cells (Extended Data Fig. 10a, b).

  It is not directly mentioned but since it's the only other "scRNA-seq dataset" used, I would assume that HT280neg_Single cell the extra Donor_7 mentioned in the table.

• for FEV1 (L) and FEV1 %Predicted you could use the new fields donor_organism.medical_tests.fev1_prebd and donor_organism.medical_tests.fev1_prebd_predicted_percent

• smoking_history I would rather use another value instead of 0 for smoking_history. Do you think the 0 value is for non-smoker?

cell suspension

• selected_cell_type the label of the ontology is type II pneumocyte however, in the OLS3 version's label is pulmonary alveolar type 2 cell. since validation is done on hcao though, there would not be a problem

analysis protocol

• alignment_software_version in the Code availability section, Cellranger version is specified as v3.1.0

[idazucchi]

thanks for reviewing!
I've updated the submission and I'm exporting

[idazucchi]

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