Roser Vento - Endometrium across menstrual cycle

[ESapenaVentura]

Primary Wrangler: @ESapenaVentura

Secondary Wrangler: TBD

Associated files:

Google Drive: https://drive.google.com/drive/folders/19JgmlhKOnQFE3wtmgJ2wVa2-TGD3pASU

Key Events

• [ ] Send initial instructions about contributing, including questionnaire and T&Cs
• [ ] Receive project questionnaire
• [x] Assign the Primary Wrangler
• [ ] Receive T&C form filled out by at least 1 representative of group/project
• [ ] Send custom metadata template spreadsheet, how-to guide and directions for submitting data files
• [x] Receive spreadsheet (to a sufficient standard to submit dataset)
• [x] Receive data (to a sufficient standard to submit dataset)
• [x] Curate metadata spreadsheet with ontologies
• [x] Upload sheet to validate metadata
• [x] Run graph validator
• [x] Check linking
• [x] Validate data files
• [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] Get final approval of submission including metadata spreadsheet and data files
• [ ] Submit to production and inform ingest-devs the project is ready for archiving
• [ ] Email UX to inform that they're ready to send survey

Please track the below as well as the key events:

1. Track date first spreadsheet received and final spreadsheet sent by editing ticket to include date next to event.
2. Track spreadsheet iterations by placing asterisks next to receive spreadsheet event.
3. Track any metadata issues/tickets made for dataset with a bulleted list of links under received spreadsheet event. Links should be to the ticket in the metadata repo.

[Wkt8]

This is now a HCA publication, see email:

Dear Roser

Thank you for submitting your recent paper entitled “Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro [biorxiv.org]” for consideration by the HCA Publications Committee.

[ESapenaVentura]

Data can be found here https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10287/

Preprint is here https://www.biorxiv.org/content/10.1101/2021.01.02.425073v1

This is an MRC + WSSS dataset

[ESapenaVentura]

We decided in a meeting that everything in the public domain is ok, so this dataset is unblocked

[ESapenaVentura]

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10287/ is undergoing maintenance to add the new file so will work on this when available

[ESapenaVentura]

Ready for secondary review!

[Wkt8]

Assigning self for secondary review

[Wkt8]

Hey! Just a few quick things: It doesn't have organoid data It doesn't have visium data (update later?) It doesn't have single-nuclei data (not available)

Donor organism tab:

• Not sure where you're getting the known diseases information but is it correct that the third individual does not have endometriosis and is infact 'normal'?

Dissociation protocol tab:

• Collagenase: Digested tissue was passed through a 100μm filter, and cells collected by centrifugation (450×g for 5 minutes at 4°C). Cells were treated with 1X red blood cell (RBC) lysis buffer (eBioscience) for 5 minutes at room temperature and washed with flow buffer (PBS containing 5% (v/v) FBS and 2 mM EDTA) prior to cell counting.
  • This can probably be moved to an enrichment protocol (cell size selection enrichment protocol with max size 100um)

Apart from that it looks good! Haven't been able to run the ingest-graph-validator on it so remember to do that when you create a submission with it!

[ESapenaVentura]

@Wkt8 about your review!

Donor organism tab:

• I got it from inferring from the name of the samples (MRC_Endo). Good eye catching the third donor, I mislabelled it!

Dissociation protocol:

• I have moved that part of the protocol to enrichment :)

I'm going to create the submission!

[ESapenaVentura]

Uploaded to ingest - No errors

Ran ingest-graph-validator: 1 error regarding analysis files, it's expected

Going to hit submit!

[ESapenaVentura]

Looks great in the browser

Closing!

[ESapenaVentura]

Updated metadata of 3 of the donors (E1, E2, E3) to normal

[ofanobilbao]

@ESapenaVentura updated and sent import form for Release 12

[ESapenaVentura]

Update looks good in the browser

[ofanobilbao]

@ESapenaVentura this is now published as peer reviewed paper.

DOI: 10.1038/s41588-021-00972-2 PMID: 34857954 https://www.nature.com/articles/s41588-021-00972-2