FoetalLungPeng

[Wkt8]

Primary Wrangler: Wei Kheng Teh

Secondary Wrangler: Ida

Associated files: Link to paper: https://www.biorxiv.org/content/10.1101/2022.01.11.474933v1.full Google Drive: https://drive.google.com/drive/folders/19zWssnTCxFEIqj1AqZDRNWFrGrOlIz8m Link to Ingest: https://contribute.data.humancellatlas.org/submissions/detail?uuid=0b53d1ad-bc5f-4030-818b-b12c7ddf5b6c&project=2fe3c60b-ac1a-4c61-9b59-f6556c0fce63

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
• [x] Send custom metadata template spreadsheet, how-to guide and directions for submitting data, matrix and cell annotation files.
• [x] Receive spreadsheet (to a sufficient standard to submit dataset)
• [x] Receive data, matrix and cell annotation files (to a sufficient standard to submit dataset)
• [x] 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
• [ ] 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.

[Wkt8]

Waiting to get additional metadata from HDBR.

[Wkt8]

Peng has mentioned that there are additional donors that he would like to add to this project, and he expects it to be in the DCP around August. Am waiting on him to send us additional information on the new donors.

[Wkt8]

Peng messaged me today saying the ATAC-seq, BCR and TCR data are ready to submit.

[Wkt8]

Wrangled scRNA, scATAC-seq, VDJ, and organoid data.

Still waiting on some metadata from Peng on the VISIUM donor metadata. Need to email HDBR to get some metadata for scATAC-seq donors.

[idazucchi]

almost done with archiving Visium data almost done with ATAC-seq data the Visum data will not be in release 12 but the rest of the data will be

[Wkt8]

We are now archiving this all in Annotare - and they have to be split up into different technologies, which has added a lot more work.

[ofanobilbao]

@Wkt8 to make 4 separate Array Express submissions, as technologies need to be separated.

[ofanobilbao]

It would be useful if he could move the files from HCA-util to annotare. @Wkt8 to create a ticket in operations

[ami-day]

There were some issues with the uploaded fastqs, Wei is looking into this

[Wkt8]

I have had to split Peng's dataset into four different ArrayExpress submissions:

• scRNA / VDJ / GEX
• Organoid
• ATAC-seq
• Visium

These have all been submitted to ArrayExpress and will have accessions to send to Peng.

The export to the DCP has not been done yet because Peng is still uncertain about the date for that to go public. The spreadsheet will be in the brokering drive. It probably will not have Visium data added to it yet due to the metadata schema change not being complete which allows imaging (probe and channel) to be optional.

Remaining actions:

• check that Peng is happy with the accessions
• complete the DCP curation (with Visium) after the metadata schema change is accepted. We could then also add the ArrayExpress accessions for the biomaterials.
• confirm with Peng a release date for the DCP curation, THEN push the dataset to be exported to the DCP
• potentially cellxgene wrangling of their processed data?

Files are available in the hca-util upload area with uuid 4777804d-1b93-4bbf-955f-1c5083e2c504

[Wkt8]

@idazucchi to sec review

[idazucchi]

Hello! I'm done with the secondary review. There is so much going on in this dataset! It's mostly good, but I have some comments Let me know if you have any question

Project

• you could add the visualisation portal link in the supplementary links section
• the grant MR/S035907/1 is repeated
• you are not listed as contributor, you really should be

Donor

• there is no donor description
• aren’t HDBR1915, HDBR2174, HDBR-N13393 HDBR donors? You could fill in the HDBR accession field
• you could fill in the gestational age for HDBR1915, HDBR2174, HDBR-N13393, from the Fetal_lung tab CS23, 8pcw, 8pcw
• the developmental stage for HDBR1915, HDBR2174, HDBR-N13393 should match their gestational age
• since the donors are fetal you should fill in gestational age instead
• you could fill in known disease as normal
• donor HDBR15415 for visium seems to be missing?

Collection protocol

• barker protocol: is it fetal donors rather than pediatrics donor?

Specimen from donor

• interesting that you applied the dissociation method for the distal/proximal specimens
• you can remove the specimens WSSS_F_LNG8713181specimen, WSSS_F_LNG8713189specimen, WSSS_F_LNG8713191specimen, WSSS_F_LNG8713180specimen, WSSS_F_LNG8713188specimen, WSSS_F_LNG8713190specimen, they are orphans
• you could fill in known disease as normal
• Whole lung
  • Is the organ part needed for the whole lung specimens? If yes maybe change whole-lung to be lung, if this is the field that gets picked up by the browser so that we don’t end up with a weird filter
  • should WSSS8012016specimen, WSSS8011222specimen have barker_lab_collection_protocol?
  • I would remove 5891STDY9030810specimen and pool the specimen at the cell suspension level
• are there other ontology terms for distal and proximal lung?
• for specimen 15415-LNG--FO-2_specimen the donor should be HDBR15415

Imaging preparation

• move the bit about freezing samples in OCT from the collection protocol to here?

Imaging protocol

• the protocol is nameless
• register permeabilisation times, maybe in the imaged specimen tab as deviation from protocol? I thought we had a field for that specifically but I can’t find it

Differentiation

• for organoid_lentiviral_induction you could add the doi 10.1101/2021.06.30.450501, the differentiation medium and small molecules

Enrichment

• the markers field for MACS_depletion is not formatted correctly
• the markers field for CD326MACS_optional_4b is empty
• you could add a mechanical dissociation protocol for whole-lung dawei 5’

Cell suspension

• for organoid and scRNA CS you could add the biosample and Insdc sample accession
• the species is missing
• the description is all right but you need to remove the formula
• 5891STDY9030810_CS should have as input specimens 5891STDY9030806_8specimen||5891STDY9030807_9specimen
• you could add the cell counts from tab scRNA and ATAC-seq CS

Library

• the libraries have no name
• the spatial barcode information is missing - do we need to update the spreadsheet template to add the spatial barcode fields or are we meant to add them manually when we need them?
• for bcr/tcr should the library construction method be 10x 5’ v1 or the immune profiling ones?

Sequencing

• the protocols have no description

Sequence file

• for organoids and scRNA: you could add the experiment and run accessions
• for all ATAC-seq: I2 files should have index2 as read index
• for SIGAA10, SIGAB10, SIGAC10, SIGAE6, SIGAF6, SIGAG12, SIGAG6, SIGAH10, SIGAH12, SIGAH4 are these sequenced with the novaSeq6000? they are not in the list in tab Fetal_Lung
• you could fill out the process id to group together the fastq files

[Wkt8]

Have made updates from Ida's secondary review, and am waiting on Peng to give an updated h5ad analysis_files

[Wkt8]

This is in graph-valid state. Can be exported.

[Wkt8]

Exporting triggered. Once it has been confirmed that the project has exported, I will fill in the DCP Import Requests form.

[ke4]

@ke4 and @jacobwindsor to investigate it

[Wkt8]

Triggered exporting again.

[amnonkhen]

@ke4 and @amnonkhen monitored the exported and found that it finished

[Wkt8]

Exported! Import Request for Production form submitted.