GSE158127 - LungTransplantationCOVID-19

[idazucchi]

Project short name:

LungTransplantationCOVID-19

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Lung transplantation for patients with severe COVID-19

• Accessioned data: GSE158127

• 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
• [x] 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
• [x] Check linking using ingest graph validator
• [x] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [x] Submit dataset to Production
• [x] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

Donor metadata the donor id in the supplementary table 1 don't match exactly the ones in GEO TX_Recipient --> Case 1 patient TX_Donor --> Case 1 donor, referred to as Donor 2 in the paper

In addition to these three [transplant] cases, lung tissue samples from other patients with lung disease were also analyzed (table S1). [ ... ]; a biopsy from a donor lung from an unrelated transplant (referred to as donor 1); a biopsy of the donor lung from the first lung transplant (referred to as donor 2);

Counterintuitively Donor 1 isn't the donor for case 1 but a lung donor from a different study

Enrichment there are some discrepancies:

1. they select CD31+ cells to isolate endothelial cells and macrophages. From the negative fraction they select.. to isolate macrophages again? doesn't make sense that they would be in the negative fraction

   The single-cell suspension was resuspended in Fc-Block (Human TruStain FcX, BioLegend) and incubated with CD31 microbeads (Miltenyi Biosciences, 130-091-935), and the positive fraction, containing endothelial cells and macrophages, was collected. The negative fraction was then resuspended in staining buffer, the volume was adjusted so the concentration of cells was always less than 5 × 107 cells/ml, and the fluorophore-conjugated antibody cocktail was added in 1:1 ratio. [ .. ] Cells were sorted on a FACSAria III SORP instrument using a 100-μm nozzle and 20 psi pressure. Macrophages were sorted as live/CD45+HLA-DR+CD206+ cells, epithelial cells were sorted as live/CD45−CD31−EpCAM+, and stromal cells were sorted as live/CD45−CD31−EpCAM− cells.

2. the selected populations in GEO are stromal, epithelial, myeloid and CD31 - no macrophage specific population

I have two guesses:

1. Macrophages were sorted as live/CD45+HLA-DR+CD206+ cells, should be myeloid cells, which is coherent with the markers used
2. PB1_4 is actually CD31 population, based on the similarities with the other CD31 samples

I've sent an email to confirm my guesses and ask for additional data for cellxgene (only the ENSEMBL ids are missing)

[idazucchi]

authors' email confirmed my guesses :)

[Wkt8]

From looking at the donor metadata, it's not very clear which patients are the 3 patients who had covid-19-associated diseases and which are the controls. Can we add something in the donor description?

e.g. Postmortem biopsy patient 1, died from severe COVID-19 Postmortem biopsy patient 2, died from severe COVID-19

Specimen_from_organism: Could use lung parenchyma for Donor1_lung? UBERON:0008946

analysis_protocol I'm not sure so wanted to double-check, is it okay to use || in the derivation_process field?

[idazucchi]

I've modified the donor descriptions and edited the organ part terms. I'm exporting the dataset