GSE128033 - ProliferatingMacrophagesPulmonaryFibrosis

ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.

https://ebi-ait.github.io/hca-ebi-wrangler-central/

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GSE128033 - ProliferatingMacrophagesPulmonaryFibrosis #891

Open ofanobilbao opened 2 years ago

ofanobilbao commented 2 years ago

Project short name:

ProliferatingMacrophagesPulmonaryFibrosis

Primary Wrangler:

~~Ami~~

Secondary Wrangler:

Associated files

Google Drive: folder sheet

Published study links

Paper: Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
Accessioned data: GSE128033

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
[ ] Upload sheet to validate metadata
[ ] Check linking using ingest graph validator
[ ] Transfer raw files to ingest to validate data files
[ ] 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

ami-day commented 2 years ago

Emailed authors to ask about donor-sample linkings. Need these to continue. thread here

ami-day commented 1 year ago

We cannot curate the data without the donor-sample linkings. The author did not get back. I will mark this dataset as ineligible and close this ticket.

idazucchi commented 1 year ago

@idazucchi reach out one last time to see if this can be moved forward

idazucchi commented 10 months ago

I found the missing metadata - it's here table 1 the only issue is that the information is missing for 2 samples SC228 and SC249 --> probably from the same donor, the seventh healthy lung donor missing from table 1

anu-shiva commented 10 months ago

Emailed authors for donor information on the two samples SC228 and SC249

anu-shiva commented 10 months ago

Wrangled the metadata. Metadata valid. Graph is invalid ingest- it shows 3 graphs errors all due to the collection protocols. Still figuring out why. But can be secondary reviewed otherwise.

anu-shiva commented 10 months ago

Graph valid!

arschat commented 10 months ago

Great work Anu figuring out how to model that unknown donor!

Specimen from organism

description for SC249NORbal_fresh is normal control, frozen although is mentioned fresh in the name & in preservation method

Collection protocol

you might be able to use BTO:0000155 "bronchoalveolar lavage" instead of biopsy for the bal collection

Dissociation protocol

dissociation_mechanical has filled the dissociation_protocol.protocol_core.publication_doi field with protocol description

Library preparation protocol

UMI BARCODE - BARCODE LENGTH (Required) for library_protocol_10x3_v1 is 10 however, should be 14

Analysis files

Genome version should be added only to the count matrix files. For cell barcode & feature table files Not Applicable should be used instead.

anu-shiva commented 10 months ago

Revised and exported. Filled out the import form.