E-MTAB-7320 - Delile2019SpatialSpinal

[idazucchi]

Project short name:

Delile2019SpatialSpinal

Primary Wrangler:

Ami

Secondary Wrangler:

Ida

Associated files

• Google Drive:

https://docs.google.com/spreadsheets/d/1fVkhUL-Gku5r8-fSIVBK-olKLzwpe_GZu75flsQ0rGo/edit#gid=1384680314

Published study links

• Paper: Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

• Accessioned data: E-MTAB-7320

• Ingest

Key Events

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

[ami-day]

Downloading fastq files.

[ami-day]

Metadata is valid in ingest, need to sync data files

[ami-day]

6f288db7-a383-441d-8c62-2b675e7e2476 --> in use be8f46d3-75b5-4c4a-a8c8-3ad678b5538f --> deleted

[ami-day]

Waiting to hear back from BioStudies about downloading matrix via ftp.

[Wkt8]

BioStudies have gotten back - needs setting up a call with them directly.

[Wkt8]

Try using wget with this link: https://www.ebi.ac.uk/biostudies/files/E-MTAB-7320/UMI_count.tsv

[ami-day]

Stuck in "metadata validating" state

[ami-day]

Sorted. Ready for secondary review.

[idazucchi]

Hi ami! I'm done with the secondary reviewing. The dataset looks good, I have only a couple of comments

Donor

• the developmental age should be more generic like embryo stage

Cell suspension

• the estimated cell count should reflect the number of cells loaded 10,000
• could you change the names of the cell suspension to sample 1 to 12 ? The cell count matrix has only barcodes + a number to identify the cell suspension so the cell suspension and barcodes can't be matched up

File sequence

• you could add the file length and the lane index

Analysis file

• you could add the cell count for the matrix

[ami-day]

Updated the metadata

[gabsie]

To be submitted today.

[MightyAx]

Stuck in data validation:

• [x] @MightyAx to use this script: https://github.com/ebi-ait/hca-ebi-dev-team/tree/master/scripts/retrigger_file_validation

[MightyAx]

Validation restarted for 12 data files.

[idazucchi]

Files validates, graph valid!

• [x] check that changes have been made

[idazucchi]

Graph valid, started exporting

[idazucchi]

exported successfully and filled in the import form

[Wkt8]

Checked. Looks good! Closing.