E-MTAB-10552 - YolkSacMultiOrganFunctions

[idazucchi]

Release date

The paper has not been published, for now the expected date for the release is January 2023

Project short name: YolkSacMultiOrganFunctions

Primary Wrangler: Ida

Secondary Wrangler:

Associated files:

• Google Drive: YolkSacMultiOrganFunctions
• Pre-print: Multi-organ functions of yolk sac during human early development
• Accessions:
  • Human embryonic liver and yolk sac 10x scRNA-seq E-MTAB-10552
  • Human embryonic yolk sac Smart-seq2 scRNA-seq E-MTAB-10888
  • Human embryonic yolk sac CITE-seq E-MTAB-11549
  • Human embryonic liver CITE-seq E-MTAB-11618
  • new - Human fetal liver CITE-seq E-MTAB-11613
  • new - Human embryonic yolk sac 10x scRNA-seq E-MTAB-11673 Ingest

Key Events

• [x] Send initial instructions about contributing, including questionnaire and T&Cs
• [x] Receive project questionnaire
• [x] Assign the Primary Wrangler
• [x] 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, matrix and cell annotation files.
• [x] Draft spreadsheet
• [x] Receive data, matrix and cell annotation files (to a sufficient standard to submit dataset)
• [ ] Curate metadata spreadsheet with ontologies
• [ ] Upload sheet to validate metadata
• [ ] Run graph validator & Check linking
• [ ] 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
• [ ] Get final approval of submission from the contributor including release date, metadata spreadsheet and data files
• [ ] Submit to production and inform ingest-devs the project is ready for archiving
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

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.

[idazucchi]

Draft status:

• [x] Human embryonic liver and yolk sac 10x scRNA-seq E-MTAB-10552
• [x] Human embryonic yolk sac Smart-seq2 scRNA-seq E-MTAB-10888
• [x] Human embryonic yolk sac CITE-seq E-MTAB-11549
• [x] Human embryonic liver CITE-seq E-MTAB-11618

I am compling a list of questions to ask but I'm waiting untill I'm done with the SS2 dataset to get the full picture

Data The dataset are already in AE and I have access as a reviewer: can I also download the data?

[ami-day]

ida needs to ask contributor about metadata

[idazucchi]

I need to :

• [x] fix the live cell selection method --> see supplementary materials
• [x] fix enrichment protocol for ss2
• [x] check facs markers
• [x] add alignment and software info for analysis check if I can download files that are not public yet with the reviewer credentials
• [x] check if we can get the h5ad files from their portal :)

I am waiting for:

• [x] sample accession for each 10x CS --> are they correct?
• [x] sequencing machine info
• [x] how many plates were used for ss2
• [x] info on the missing fastq from the barcode file accession E-MTAB-10888

[idazucchi]

I am in active communication with the authors but I still have not recieved the information above

[idazucchi]

the lab is in the process of submitting their manuscript so they have reduced availability, I will contact them again in ~4 weeks

[idazucchi]

I've updated the HCA spreadsheet with the CS/enrichment metadata they've sent me.

I am still waiting on two other people to get back to me about:

• [x] total of sequence files
• [ ] new analysis file?
• [x] 10x version used - manifest and AE disagree
• [x] sequencing machine used for each file

[MightyAx]

email response received, updated pending

[idazucchi]

I recieved a link to the pre-print and I have updated most of the information I had in the spreadsheet. I still need to check ss2 data and the grants tab

to do next:

• [ ] wrangle the 2 new accessions
• [ ] get in touch so the authors can review the spreadsheet
• [ ] get the fastq files --> directly from sanger?

[ofanobilbao]

@idazucchi are we still blocked on this? Does not look like right?

[ofanobilbao]

@idazucchi to check if the data is already public. If not, not worth investing time.

[idazucchi]

the data is live! I can finish wrangling this, we just have to decide how to prioritise

[idazucchi]

I've emailed the authors so they can review the project so far + to confirm 2 more accessions are part of the project

[idazucchi]

I've wrangled the 2 additional accessions

todo:

• [ ] add files for 10x - waiting on authors to advise on conversion or originals
• [ ] ontology
• [ ] validation

[idazucchi]

I got in touch with the BioStudies team to see if they can help with downloading the fastq files for E-MTAB-10552 since the links are broken

[idazucchi]

Downloading data from globus

[idazucchi]

Download of data is complete

next steps:

• [ ] prepare hca-util area
• [ ] validate project
• [ ] get approval for publishing? is there an official publication now?
• [ ] secondary review