Contributor - AdultHumanBrain

[ESapenaVentura]

Project short name:

AdultHumanBrain

Primary Wrangler:

Ida

Secondary Wrangler:

TBD

Associated files

• Google Drive: folder

Published study links

• Paper: Transcriptomic diversity of cell types across the adult human brain

• Accessioned data: http://data.nemoarchive.org/biccn/grant/u01_lein/linnarsson/

• Ingest project: https://contribute.data.humancellatlas.org/projects/detail?uuid=f8888f5a-4a19-41d0-ad96-4fafce8a8e79

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
• [ ] Transfer raw files to ingest to validate data files
• [ ] Check linking using ingest graph validator
• [ ] 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

[idazucchi]

Fastq The data in nemoArchive is stored in a tree structure, with high level directories named after the 10x sample id. The samples are described in the supplementary table 1. Problem: there are 606 samples in the metadata, but just 260 directories in nemo -> I'm sending an email asking for clarification

In the meanwhile I'm filling in the biomaterial and protocol tabs, and mapping the organ part terms to the ontology (very specific neuroanatomy I'm not familiar with so it will take some time)

[idazucchi]

Peter confirmed that some fastq files are missing and the project is on hold until this is resolved (thread)

[idazucchi]

All the data is in Nemo right now, but the project has lower priority than Lung v2. I've sent an email to Peter to ask for neuroanatomical term mappings before I proceed with the work anyway

[idazucchi]

Data All the fastq files have been uploaded to Nemo, however the majority are under restricted access, so I still don't have full access to the raw files. I've just emailed Peter about this to see if it's intentional or if there is a different way to download the data.

Organ part ontology I've mapped all the organ part terms manuallly and sent the list for review - see it here

This is stalled untill I have access to the raw files

[idazucchi]

the authors sent back comments on the neuroanatomical term mappings but no information on fastqs access, so I'm still stalled

[idazucchi]

neuroanatomical term I checked the neuroanatomical term mappings and found that one term suggested by the authors is in OLS but not in HCAO - anterior cortical amygdaloid nucleus (UBERON:0034991)

if we'll be phasing out HCAO soon there's no point in opening a ticket about this issue

fastqs I pinged Peter again to see if we can get access to all fastq files

[idazucchi]

I'm trying to download the files again, it looks like they've become available now