EGAS00001004653 - PancreasTopographiesTosti10x

[arschat]

Project short name:

SPAN PancreasTopographiesTosti10x

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder
• ingest: b3938158-4e8d-4fdb-9e13-9e94270dde16

Published study links

• Paper: 10.1053/j.gastro.2020.11.010
• Accessioned data: EGAS00001004653
  supl_link

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]

Dataset has been partially wrangled, but it contains invalid metadata. Should be revised and resubmitted as is part of Pancreas bionetwork list.

[arschat]

Seems that project was partially wrangled by Ami, but abandoned because no sequence or analysis files were available at that time #827
Now analysis files are available at http://singlecell.charite.de/pancreas, I've downloaded them and start wrangling dataset again.

[arschat]

Removing previous submission since it had not being published before.
Spreadsheet saved here.

[arschat]

hca-util area 39d07165-5711-4c82-870a-7496214fde73

I added the schema tab in the spreadsheeet to specify the version of the files that allows the validation (until EDAM update is completed).

[arschat]

Graph valid and ready for sec review!

[idazucchi]

Hi!
Nice job on this dataset, I have only a couple of small comments

Donor / Specimen

• I think the disease for TUM_13_donor could be pancreatic neuroendocrine neoplasm since the tumor is reported as a pancreatic disease
• for donor TUM_C1_donor : From this paper it sounds like Mixed Muellerian Tumor is a malignant tumor affecting the uterus that can rarely develop metastasis in the pancreas. I would suggest carcinosarcoma in place of adenofibroma because adenofibroma has benign mixed Muellerian tumor as synonym.

Collection protocol

• shouldn't Standford_protocol be collecting specimen from organ postmortem? the donors are dead at collection time

Cell suspension

• very minor -but- should we change the description to Nuclei suspension?

Analysis file

• input CS for chronic_* files should be TUM_CP1_nuc and TUM_CP2_nuc

[arschat]

Nice catch on the wrong CS for the chronic_* files! Thank you for the review. I applied all changes to the submission, and is now exported!

• import form sent

[arschat]

Noticed a flip of diseases for donors TUM_25_donor and TUM_C1_donor. Replaced that in staging area's metadata jsons.

1. Copied contents of the json files

gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json

2. Created locally the files and flipped the diseases field with text editor
3. Uploaded edited files to staging area

gsutil cp 2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
gsutil cp 0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json

4. I updated both biomaterials in ingest as well TUM_25_donor, and TUM_C1_donor
5. change status to exported

• it was indeed a mistake:
  • TUM_C1_donor has to have pancreatic ductal adenocarcinoma and it had carcinosarcoma -> Mixed Muellerian Tumor
  • TUM_25_donor has to have carcinosarcoma -> Mixed Muellerian Tumor and it had pancreatic ductal adenocarcinoma