Adult_Nonmobilised_PB Laurenti submission: track progress

[ami-day]

Primary Wrangler: Ami

Secondary Wrangler: Enrique

Associated files: https://docs.google.com/spreadsheets/d/1j1UZ7nc6U-BgVz0xZSHipkxHE9t-vbdXUVEkr2SVQ3A/edit#gid=900688680

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 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
• [x] 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.

[ami-day]

@ESapenaVentura this spreadsheet is ready for review. I made changes to the original and filled ontologies but have not added it to ingest yet, I will after we have reviewed and updated it. Some comments: please could you in particular check the selected cell types and also dissociation methods. There are multiple values so I added "||" between them, but the fill_ontologies.py script is adding just 1 ontology label and term. Thank you!

[ESapenaVentura]

I have reviewed the spreadsheet and saved the result as <spreadsheet_name>_Enrique_review.

Donor organism

• Changed “cause of death” from “not applicable” to blank

  Collection protocol

• Looking at the name and description of the collection_protocol_2 - Maybe we should request to add pheresis to the ontology terms under blood draw? Blood draw is correct in this case but it’s inaccurate

  Dissociation protocol

• Changed the dissociation protocol from “blood_draw” to “density gradient dissociation”, changing name, description and method text, ontology and ontology_label

  Cell suspension

• Added "hematopoietic multipotent progenitor cell” (CL:0000837) in selected cell type property. We should discuss with them if they feel this is a right term to describe “progenitor cell”.
• Deleted “plate label”. This is a 10x experiment, so well-related properties do not make sense here

  Sequence file

• We need to ask them about the library_preparations. If they sequenced the same library prep several times (as the metadata indicates) we need to specify the lane_index. If not, we can change the processes to specify the different library preps

  Sequencing protocol

• Changed paired_end to “no"

[ami-day]

Thank you @ESapenaVentura!

I had the same thought about this: 'Maybe we should request to add apheresis to the ontology terms under blood draw'. I actually added that term then ran your fill_ontologies script, and there is not an appropriate ontology term for it, so I changed it back to blood draw. It is still kind of a blood draw though so I think it is ok, given they describe the process in the collection protocol description.

The other changes sound good.

I agree with your queries; I'll respond to them today with some questions about these and also send them the HCA questionnaire. I'll reply to Hugo separately about the bam files so I can respond to Elisa/the group.

[ami-day]

Could you please paste the link to the questionnaire here? Is it possible to change the template dataset issue tickets to include the HCA T&Cs link and the questionnaire link?

[ESapenaVentura]

http://tinyurl.com/HCA-Terms-Conditions

Sure, if you feel like it will be better there you can create a ticket and, in a new branch, suggest changes to the templates, and the rest of the wranglers can review the PR :)

Also, there is an error in my comment, sorry: For the dissociation protocol, I deleted it*

[ami-day]

@ESapenaVentura that link is for the terms and conditions form! What is the link to the questionnaire?

[ESapenaVentura]

Completely misread that, sorry!

http://tinyurl.com/HCA-Project-Questionnaire

[ESapenaVentura]

Changelog 12th June 2020:

• Renamed cell suspensions to same name + CS to distinguish the names from the specimens.
• Corrected datetime for colletion of all specimens (Incorrect format)
• We need to correct the preservation method, it's currently invalid. An email asking for the preferred option from the enum list would be great

[lauraclarke]

Does this ticket need to continue to exist or do we need a ticket to track the datasets which need to be exported to DCP2 as wrangling is now done if I understand it correctly?

[lauraclarke]

Actually, I remembered the GDPR question, does this dataset contain living donors? if it is, we can't push it to the DCP

[ESapenaVentura]

@lauraclarke yes, this dataset does contain living donors ~(As well as the previous Laurenti's dataset)~ Not sure about the previous one.

[lauraclarke]

I thought the previous one was deceased donors rather than living ones?

[ESapenaVentura]

This dataset is already wrangled, right?

Can we close it?

[ami-day]

This project is stalled due to it involving samples from living donors.

[ami-day]

Hugo has new donors and samples to add so this project is being updated. @aaclan-ebi is working on some ingest fixes and then will start working on archiving this.

[aaclan-ebi]

Thanks @ami-day for providing me the spreadsheet.

I used the spreadsheet here: https://docs.google.com/spreadsheets/d/1HMfdXl2LSYDDb4Etjgg1jJZpMe3oYFYG/edit#gid=668357357 (i renamed it to 2020118_SUBS10_PB_extra_donors_hca_spreadsheet_edit.xlsx)

Here's the new submission in prod https://contribute.data.humancellatlas.org/submissions/detail?id=6005bd74c9762f5f0de9f6c9&project=fc55bd4a-8694-4a28-9a35-59a685bda323

Project's page: https://contribute.data.humancellatlas.org/projects/detail?uuid=fc55bd4a-8694-4a28-9a35-59a685bda323

If it looks good, would you be able to upload the files for this submission? Thanks!

[ami-day]

We also need to update the project description to include the new cell and sample count. But we need to wait for other changes/fixes first.

[ami-day]

Have uploaded the data files to the submission.

[aaclan-ebi]

We've fixed some linking issues in the dataset. New spreadsheet: https://docs.google.com/spreadsheets/d/1-O9tnP_AdO7RejP33Yy9iKUe-Z27AI9a/edit#gid=1768425982 New submission: https://contribute.data.humancellatlas.org/submissions/detail?id=600715e4c9762f5f0de9fa67&project=fc55bd4a-8694-4a28-9a35-59a685bda323 Awaiting file upload @ami-day . Thanks!

[aaclan-ebi]

Current DSP Submission: https://submission.ebi.ac.uk/api/submissions/74d16604-6a2c-497e-b1ca-1e552c30cfcf

Summary of entities to be archived: 6 samples (2 donors, 2 specimens, 2 cell suspensions) 2 sequencing experiments 16 sequencing runs

See details: https://api.ingest.archive.data.humancellatlas.org/archiveSubmissions/6008584cc9762f5f0de9ff3c/entities?size=24

The file archiver jobs are currently running in the EBI cluster. We'll complete the submission once all jobs are done and submission is valid.

[aaclan-ebi]

Hi @ami-day

We've completed the DSP submission and here are the accessions :

SAMEA8072986
SAMEA8072985
SAMEA8072987
SAMEA8072988
SAMEA8072984
SAMEA8072983
ERX4972373
ERX4972372
ERR5167451
ERR5167449
ERR5167445
ERR5167442
ERR5167447
ERR5167446
ERR5167448
ERR5167450
ERR5167444
ERR5167452
ERR5167441
ERR5167439
ERR5167443
ERR5167440
ERR5167438
ERR5167437

Could see more details on the entities here: https://api.ingest.archive.data.humancellatlas.org/archiveSubmissions/6008584cc9762f5f0de9ff3c/entities?size=24

[ami-day]

This is great @aaclan-ebi :) Can we edit the project description still to reflect the additional cells & samples since the 1st submission was submitted?

[aaclan-ebi]

Yup, i'll look into that today.

[aaclan-ebi]

@ami-day could you paste here the exact update to the project description here:

current value:

Haematopoietic stem and progenitor cells (HSPCs), the precursors of all blood cells, reside predominantly in the bone marrow. Yet, a  small proportion (<1%) of phenotypic HSPCs circulates through peripheral blood (PB) at any given time. To date, the detailed characterization of steady-state circulating HSPCs in adult humans remains very poor. Here, we analyse the single-cell composition of the adult human HSPC pool within non-mobilised PB from four healthy donors. 10x scRNA-seq of 22000 HSPCs from all four donors was paired with single-cell functional analysis using most immature haematopoietic stem cells and multipotent progenitors (HSC/MPPs). We find that long-term functional HSC/MPPs are very rare in non-mobilised PB, and that a large fraction of circulating HSPCs is biased towards the erythroid lineage. In particular, we detect the enrichment of a subset of exclusively erythroid/megakaryocyte-primed quiescent HSC-like cells within the phenotypic PB HSC/MPP compartment.

After a call with Karoly (DSP), we decided to do it manually via BioStudies and ENA UI (pending approval from Melanie) to avoid any issues in updating via DSP. It's just 2 simple updates to project & study so it's not painful to do it manually via BioStudies & ENA UI. DSP is going to be deprecated soon so I'd say the discrepancy between DSP and archives is acceptable. We just need to make sure it's noted. If ever we need to make more updates while using DSP.

[ami-day]

New value:

Haematopoietic stem and progenitor cells (HSPCs), the precursors of all blood cells, reside predominantly in the bone marrow. Yet, a  small proportion (<1%) of phenotypic HSPCs circulates through peripheral blood (PB) at any given time. To date, the detailed characterization of steady-state circulating HSPCs in adult humans remains very poor. Here, we analyse the single-cell composition of the adult human HSPC pool within non-mobilised PB from four healthy donors. 10x scRNA-seq of 51,000 HSPCs from all six donors was paired with single-cell functional analysis using most immature haematopoietic stem cells and multipotent progenitors (HSC/MPPs). We find that long-term functional HSC/MPPs are very rare in non-mobilised PB, and that a large fraction of circulating HSPCs is biased towards the erythroid lineage. In particular, we detect the enrichment of a subset of exclusively erythroid/megakaryocyte-primed quiescent HSC-like cells within the phenotypic PB HSC/MPP compartment.

Thanks @aaclan-ebi !

[aaclan-ebi]

Thanks @ami-day

Karoly(DSP) and I couldn’t use the DSP username+password for the BioStudies UI. It seems like it uses a different email and password. I emailed biostudies@ebi.ac.uk to request for the update: biostudies #475915 ( cc'ed you) Let's just keep an eye on it.

[aaclan-ebi]

Karoly is also looking into updating it in ENA Web in portal but their UI is very slow and he couldn't proceed. He's checking with some ENA folks for help.

[aaclan-ebi]

Filed an issue to ENA regarding the issue on their webin UI.

[aaclan-ebi]

@ami-day ENA study is already updated https://www.ebi.ac.uk/ena/browser/view/PRJEB38994

[aaclan-ebi]

@ami-day BioStudies project is already updated https://www.ebi.ac.uk/biostudies/studies/S-SUBS10?query=S-SUBS10

[ofanobilbao]

@ami-day I have added the SCEA brokering label, assuming this needs to be brokered to SCEA. Please, remove if that's not the case. I have moved it to Finished on the wrangling board as from what I can see it looks like Done from a DCP point of view. Is that correct? Please, let me know or move it as you deem appropriate. Thanks!