GSE162610 - Milich2021MouseSpinal

[ofanobilbao]

Project short name:

Milich2021MouseSpinal

Primary Wrangler:

Ida

Secondary Wrangler:

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=e6773550-c1a6-4949-8643-1a3154cf2670&tab=project

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord

• Accessioned data: GSE162610

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
• [ ] 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]

Sample design

One sample from each time point consisted of cells from a single spinal cord. In all other samples, cells were pooled from two animals. In total, we sequenced three uninjured biological replicates (from five animals), three biological replicates at 1 dpi (from five animals), two biological replicates at 3 dpi (from three animals), and two biological replicates at 7 dpi (from three animals). We enriched our second set (and third set for uninjured and 1-dpi samples) of replicates with astrocytes by pooling from two spinal cord samples. We processed two spinal cords from each injury time point in parallel as described above to yield two suspensions per time point.

[idazucchi]

close to done I'm converting bam files to fastq

to do:

• [x] file tab
• [ ] ontologies
• [ ] validation

[idazucchi]

graph valid, redy for secondary review

[gabsie]

@ami-day will secondary-review

[ami-day]

This looks really good @idazucchi . I have only a couple of comments:

• The 3 sequencing protocols look the same, should there just be 1 protocol id linked to all the cell suspensions?
• They enrich for astrocytes in some cases, the selected cell type could be filled for the relevant cell suspensions in the cell suspension tab

A general question I have for recent prioritised datasets: should we be selecting "official hca publication" given that the prioritised datasets are part of hca networks?

[idazucchi]

the sequencing protocols differ in the cell ranger version used for the astrocytes I'm not sure how to approach this beacause they mix 1 astrocyte-selected cell suspension + 1 non enriched cell suspension so it's not strictly astrocytes

I don't think that we should be using the official hca publication option for the bionetworks datasets because the papers for the two groups are selected in different ways and are not equivalent

[idazucchi]

I've exported the dataset and filled out the import form

[ofanobilbao]

Ida made the required changes to remove the double pipes that were causing issues to the browser. She re-exported and filled out the import form. This was one of the projects that has been dropped from DCP while we resolved the issues