GSE144469 - inflammationInducedCancerImmunotherapy

[arschat]

Project short name: inflammationInducedCancerImmunotherapy

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Associated files

• Google Drive: folder

Published study links

• Paper: 10.1016/j.cell.2020.06.001

• Accessioned data: GSE144469 ingest: 3373e59c-525f-4a83-8c9c-d8b280454697

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

[arschat]

Message from Will:

GSE144469 - Gut Dataset

• Metadata spreadsheet
• Upload area - 798fd266-9da6-43f9-8104-396cde029fdc For some reason hca-util upload keeps failing every time I try to upload the files

[idazucchi]

collection protocol

In all cases, biopsies were obtained during endoscopy using a standard-of-care forceps, spanning the regions from the descending colon, sigmoidal colon, and rectum; for two patients, C2 and NC2, biopsies from the ascending colon were also collected. Typically, 2-6 biopsies from each region were separately allocated into DMEM media and transported on ice to the lab for immediate tissue dissociation. For some patients (n = 4 control, n = 1 +CPI no colitis), descending, sigmoid, and rectum biopsies were collected as a single pool rather than separately from each region.

We have info on which regions samples are collected from but not how many specimens or how they were pooled, so I'm representing each sampled location with one specimen

The supplementary tables offer quite a bit of metadata on the donor's treatment, but we don't have a good way of capturing it, other than squeezing it all in the treatment section. I've decided to add a supplementary table instead because I think it will make it more usable

[idazucchi]

files stuck in validation, will re-trigger with the script

[idazucchi]

file validated and graph valid!

[arschat]

Hi Ida, excellent work on that! I agree with the modelling. I have only two comments, on an ontology mapped and the genome version of a file.

• We prefer using MONDO ontologies compared to HP. The definition of diarrhea disease for mondo is

  The condition of having at least three loose or liquid bowel movements each day.

  According to the Table S3 donors who have diarrhea have CTCAE grade >= 1. Finally, according to this pdf, CTCAE grade means

  Increase of <4 stools per day over baseline; mild increase in ostomy output compared to baseline

  Given that, I would use the MONDO term rather than the HP one here. I understand that it's prone to interpretation though.

• The contig_annotation files should have a Genome version or it is Not applicable? The first file GSM4560096_C1-gdTCR_filtered_contig_annotations.csv.gz has Not applicable, while all other gdTCR and abTCR files have the GRCh38 version.

[idazucchi]

applied suggestions, exported and filled in import form