SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

ipediez commented 2 years ago

Project short name:

CovidCellTypes

Primary Wrangler:

Ami

Secondary Wrangler:

Irene

Associated files

Google Drive https://docs.google.com/spreadsheets/d/1WiPlkBzBZBrCu4SbOt2uGCe0vIxE-bGHvB5WKrI_Rdo/edit#gid=817397388

Google Sheet https://docs.google.com/spreadsheets/d/1WiPlkBzBZBrCu4SbOt2uGCe0vIxE-bGHvB5WKrI_Rdo/edit#gid=1646211853

Ingest: Updated link to project with submission --> project

Published study links
Paper: https://doi.org/10.1016/j.cell.2020.04.035

NOTE: in the paper supplementary files, they note the analysis of already published datasets from a previous study. We didn't have that study in ingest, so I have added it as a separate project using the paper doi: Ingest: ~~https://contribute.data.humancellatlas.org/projects/detail?uuid=326b36bd-0975-475f-983b-56ddb8f73a4d&tab=project~~ Paper: https://www.nature.com/articles/s41586-018-0449-8#Sec2

Accessioned data: mouse (GSE148829), other (https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project)

Key Events

[x] Convert published metadata to HCA spreadsheet
[x] Manually curate dataset to meet HCA metadata standard
[ ] 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
[x] Submit dataset to Production
[ ] Complete the Export SOP
[ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

ipediez commented 2 years ago

Taking this dataset for secondary review

gabsie commented 2 years ago

@ipediez will review today

ipediez commented 2 years ago

Project

Estimated cell count is missing. From Table S9 I took the information of the unpublished results and "This study" results, and summed up the cells stated there. You could check this and add the total number of cells as estimated cell count.
- Human Adult Inferior Turnibate Scraping (SeqWell1 and 3): 10.111 cells
- Mouse nasal mucosa (seqWell 3): 11.738 cells
- Human ileal small intestine (10x v2 3'): 22.220 cells
- Human lung (seqWell 3): 1.637 cells
- I haven't found the information for Mouse_cell_line_donor and Human_cell_line_donor.
Don't forget to update the information in Ingest about the project, as you have much more information in the spreadsheet😉

Donor

For the mice receiving IFNa or saline solution, add the timecourse information. This would be a time course value and unit of 12 hours, and the relevance would be something like "sacrifice after treatment with 200ng of IFNa" or "sacrifice after treatment with saline solution", respectively.

Specimen from organism

Although it is gonna work in ingest and it is gonna link correctly the biomaterials, you have entered cell suspension IDs on the specimen_from_organism.biomaterial_core.biomaterial_id column. It would be better to add a new column cell_line.biomaterial_core.biomaterial_id and input there the cell lines. You can easily do this by copying the first column at the Cell line tab and inserting it at the Cell suspension tab. You can do this to make the modelling more ordered, or just leave it as it is.

ami-day commented 2 years ago

Thanks @ipediez really good points! The last one was a mistake, i would usually model it as you said re: the cell line and specimen ids in the cell suspension tab.

ami-day commented 2 years ago

I checked the cell count estimates by comparing to the GEO matrix cell counts. The values pretty much correspond, with some discrepancy as expected because of quality filtering of the data post cell sorting and library preparation.

The cell counts you were unable to find makes sense because they are bulk samples that were sequenced, hence no single-cell estimates.

Here is a table just fyi of the cell counts. I have entered 33,844 as the total cell count in the project tab.

ami-day commented 2 years ago

Going forward, I have decided that when the matrices are available, I will always use the matrix cell count (now I have a script to calculate this quickly direct from a gzip file). This is because I incorrectly way overestimated a project count recently, due to misreading individual sample counts in the paper. When various technologies arenused, it's easy to do. I find the matrix column count for me at least will be less error prone!

ami-day commented 2 years ago

Emailed the authors about cell types annotation.

ami-day commented 2 years ago

PRJNA627454 files are downloading in tmux session, data scripts folder on EC2.

ami-day commented 2 years ago

ed164273-b241-4cd7-9263-eae87cbd33b1

ami-day commented 2 years ago

synced the data

ami-day commented 2 years ago

graph validating

ami-day commented 2 years ago

Submitted to HCA DCP.

ami-day commented 2 years ago

exported to hca dcp.

MightyAx commented 2 years ago

R16 ReExport Successful

ESapenaVentura commented 2 years ago

This project is repeated 3 times in ingest
- Actual project is not the one indicated in ingest but this one https://contribute.data.humancellatlas.org/projects/detail?uuid=0b299140-25b5-4861-a69f-7651ff3f46cf&tab=project
- Please delete the other 2, transfer the metadata (technology, organ etc) to the project that contains the submission and tick the "isInCatalogue" flag
The supplementary links are not formatted correctly (Long string separated by ; instead of array of strings)

ami-day commented 2 years ago

This project is repeated 3 times in ingest

Actual project is not the one indicated in ingest but this one https://contribute.data.humancellatlas.org/projects/detail?uuid=0b299140-25b5-4861-a69f-7651ff3f46cf&tab=project

Please delete the other 2, transfer the metadata (technology, organ etc) to the project that contains the submission and tick the "isInCatalogue" flag

The supplementary links are not formatted correctly (Long string separated by ; instead of array of strings)

Ok done, the graph is re-validating.

ami-day commented 2 years ago

Re-submitted.

ami-day commented 2 years ago

Exporting.

ami-day commented 2 years ago

It seems to have got stuck in exporting: https://contribute.data.humancellatlas.org/projects/detail?uuid=0b299140-25b5-4861-a69f-7651ff3f46cf&tab=upload

Wkt8 commented 2 years ago

Check if the dataset has been fully exported, if it has, then to set it back to valid to allow for further update. needs looking into and creating a bug ticket for why the state tracker is failing to properly capture states of datasets.

ESapenaVentura commented 2 years ago

SOP here

Wkt8 commented 2 years ago

There's not a further update that needs to be done for this dataset - if it is fully exported, set the state to exported, and then this can be moved to done.

ami-day commented 2 years ago

Already created the ticket, it is in the Operations board

ESapenaVentura commented 2 years ago

One export job was aborted due to a connection error:

2022-07-25 12:39:15 
{"log":"2022-07-25 11:39:15,689 - exporter.terra.terra_listener - ERROR - submission_uuid:302c1f08-dc2d-4653-8a43-e8ff5ac5d9f0 - export_job_id:62de808a5cc3b03957ee841d - ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n","stream":"stderr","time":"2022-07-25T11:39:15.693895467Z"}
2022-07-25 12:39:15 
{"log":"2022-07-25 11:39:15,686 - exporter.terra.terra_listener - ERROR - submission_uuid:302c1f08-dc2d-4653-8a43-e8ff5ac5d9f0 - export_job_id:62de808a5cc3b03957ee841d - Rejecting export experiment: ExperimentMessage(process_id='626122b94770e410d1f2089a', process_uuid='9f502e93-ba47-44dc-ba90-224d753677e3', submission_uuid='302c1f08-dc2d-4653-8a43-e8ff5ac5d9f0', experiment_index=73, total=82, job_id='62de808a5cc3b03957ee841d') due to error: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n","stream":"stderr","time":"2022-07-25T11:39:15.686507103Z"}

MightyAx commented 2 years ago

the project link above no longer exists

ami-day commented 2 years ago

It is still stuck in exporting: https://contribute.data.humancellatlas.org/projects/detail?uuid=0b299140-25b5-4861-a69f-7651ff3f46cf&tab=upload

MightyAx commented 2 years ago

This was really old so was a bit harder to find but we just needed to retry this message

Rejecting export experiment: ExperimentMessage(process_id='626122b94770e410d1f2089a', process_uuid='9f502e93-ba47-44dc-ba90-224d753677e3', submission_uuid='302c1f08-dc2d-4653-8a43-e8ff5ac5d9f0', experiment_index=73, total=82, job_id='62de808a5cc3b03957ee841d')

I published this message again using the rabbit admin interface, the export succeeded and the project has been set to exported (even after a month of waiting)

{"exportJobId":"62de808a5cc3b03957ee841d","documentId":"626122b94770e410d1f2089a","documentUuid":"9f502e93-ba47-44dc-ba90-224d753677e3","callbackLink":"/processes/626122b94770e410d1f2089a","documentType":"process","envelopeId":"626122334770e410d1f2034c","envelopeUuid":"302c1f08-dc2d-4653-8a43-e8ff5ac5d9f0","projectId":"626122464770e410d1f2034e","projectUuid":"0b299140-25b5-4861-a69f-7651ff3f46cf","index":73,"total":82,"context":null}

ami-day commented 2 years ago

Ok submitted import form for update.

ami-day commented 1 year ago

looks ok

ebi-ait / hca-ebi-wrangler-central