GSE158055 - COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

[ofanobilbao]

Project short name: dcp1738124286382552 (tbc by wrangler)

Primary Wrangler:

Wei

Secondary Wrangler:

Ida

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=5f607e50-ba22-4598-b1e9-f3d9d7a35dcc&tab=project

Associated files

• Google Drive:

Published study links

• Paper: https://doi.org/10.1016/j.cell.2021.01.053

• Accessioned data: GSE158055

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

[Wkt8]

Created upload area with UUID "34a9a5fd-316b-4155-b5ea-ac6d6090d224" and name covidimmunefeatures

[ofanobilbao]

It was stuck in Graph validating. Can't check now as Ingest login not working

[Wkt8]

Ingest login now working. Still stuck in graph validating. >24hrs.
https://contribute.data.humancellatlas.org/submissions/detail?uuid=3b404659-807f-4095-940b-2873f56cafd7&project=5f607e50-ba22-4598-b1e9-f3d9d7a35dcc

[gabsie]

@MightyAx could check

[MightyAx]

• Reset submission back to draft (restarted state tracking)
• re-validated project
• Set submission to Valid (restarted state tracking)
• triggered graph validation
• wait for success

[MightyAx]

This project is ready to submit

[ofanobilbao]

Thanks @MightyAx . The projects is ready for secondary review

[idazucchi]

Hello! I've done the secondary review, the project looks good but I have number of minor comments

Project

• change the short name to something readable
• add supplementary link to portal http://covid19.cancer-pku.cn
• add yourself as data curator!

Donor

• add donor description
• it would be nice to record the time passed since the disease onset. Unfortunately we can't add the timecourse on the specimen level (I've added it to the metadata schema updates ticket), but you could add it to the donor level
• is there somewhere we can record the disease outcome? description?

Specimen

• add specimen description
• you can add the storage method to distinguish fresh/frozen PBMCs

Dissociation

• Sputum_processing is mechanical dissociation in my opinion

Enrichment

• add the FACS/MACS protocols for CD19+ and CD3+

Cell suspension

• missing cell suspension description
• some CS are missing the FACS/MACS enrichment protocol and can have a more specific cell type, like B or T cell
• growth_medium should not be filled in
• S-M074-1_CS has 3 free text cell types, but 2 ontologised terms
• for BALF I would suggest epithelial cell of lung rather than epithelial cell of alveolus of lung

Library prep

• missing primer
• 10x 5' library should have 5 prime tag as end bias

Sequencing protocol

• missing description and name

Analysis protocol

• you could add the software used for the analysis in the computational field
• derivation process is empty for raw_matrix

Analysis file

• you can add the cell count for the matrix
• you can add the h5ad files from http://covid19.cancer-pku.cn/#/summary

[Wkt8]

Edited and resubmitted to Ingest. Now Graph Validating.

[Wkt8]

Graph valid!

• Export
• Import form sent

[ESapenaVentura]

This dataset needs 2 updates before goes live:

• Description of donors is a formula (Be careful with that, openpyxl does not translate formulas the way excel does! if you want to use formulas you have to later just copy --> paste value)
• Donor P-M032 does not have an age associated with the donor (But has age unit)

I am currently fixing them

[idazucchi]

Enrique will restart graph validation

[gabsie]

hey @ESapenaVentura - did you try this out today? Just checking

[ESapenaVentura]

submission is in metadata valid - Ingest is not currently working

[ESapenaVentura]

Submission is exporting - CUrrently in queue

[ESapenaVentura]

I think it failed export - No new messages from the exporter since 2 hours ago (When it started)

[idazucchi]

To be exported for R26

[Wkt8]

Stuck in exporting

[ESapenaVentura]

Needs update to project contributors

[ofanobilbao]

Version with corrected double pipes was exported by Amnon yesterday, 22/05/2023. Arsenios filled out the import form

[Wkt8]

Looking for this in the link for : https://data.humancellatlas.org/explore/projects?catalog=dcp28 and I cannot find the project.

[Wkt8]

Verified