A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.

[ipediez]

Project short name:

FreshFrozenHumanTumours

Primary Wrangler:

Ami

Secondary Wrangler:

Irene

Associated files

• Google Drive: https://drive.google.com/drive/folders/1EZONxSWvdqrdUZU4Hn4CMLPEOVBgCtX6

• Google Sheet: https://docs.google.com/spreadsheets/d/1mUt7-zupyi_4rk0XGnqrutQJd1LjjmUkmBVyXBJrBGc/edit#gid=1612993960

• Ingest: https://contribute.data.humancellatlas.org/projects/detail?uuid=5850583c-baec-4427-8656-cd3c96c07727

Published study links

• Paper: https://doi.org/10.1038/s41591-020-0844-1

• Accessioned data: GSE140819 and phs001983

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] Upload sheet to validate metadata
• [ ] Check linking using ingest graph validator
• [ ] Transfer raw files to ingest to 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
• [ ] Submit dataset to Production
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[ami-day]

Requested ontology term for specimen collection process: https://github.com/HumanCellAtlas/ontology/issues/108

[ami-day]

Have sent the authors an email to get some clarifications.

[ipediez]

LGTM, good job on this project! I just have three small comments:

Project:

• Add the estimated cell count. They stated it in the abstract of the paper, therefore it's also available in the project description in ingest.

Donors:

• Why do donors MGH123 and HTAPP-443-SMP-5491 have two different development stages? According to https://tumor-toolbox.broadinstitute.org/ HTAPP-443-SMP-5491 is pediatric and I can't find the information for MGH123

Specimen from organism:

• Some of the organs are set as "waiting to hear from author". Did you get a response from the authors?

[ami-day]

Thanks @ipediez

• I added the estimated cell count

• I changed the development stage to "child stage" for those 2 samples you mention. I re-read the methods, and it looks like all the glioma samples were from a children's hospital.

• I changed "waiting to hear from author" to "nervous system". If I hear back with something more specific once submitted, I will update the dataset. I haven't heard anything back.

[ami-day]

graph validating

[ami-day]

Submitted.

[ami-day]

Exporting.

[Wkt8]

Exported.

[ESapenaVentura]

Looks ok in the browser, however:

The project is duplicated in ingest. The actual project + submission is here https://contribute.data.humancellatlas.org/projects/detail?uuid=a62dae2e-cd69-4d5c-b5f8-4f7e8abdbafa and it's missing:

• technology info
• organ info
• flag to be in catalogue
• admin info

I will add them for now to move from here but please stop creating duplicate projects, use the ones that exist

[ESapenaVentura]

Actually, it was missing publication PMID and doi so I would rather update it

[ami-day]

Re-exported with @ESapenaVentura 's update. Submitted import form for update.

[ami-day]

Looks ok in DCP Data Browser

[ESapenaVentura]

Moving to needs update: as stated in this message https://embl-ebi-ait.slack.com/archives/C9XD6L0AD/p1660584420081069 the ontology_label terms for lung and blood need to be changed to lowercase

[ami-day]

Made update to lung, blood, ovary labels (upper case to lower case)

[ami-day]

Graph validating

[ami-day]

Submitted in ingest.

[ami-day]

Form submitted.

[ami-day]

looks ok

[ami-day]

looks ok