GSE159745 - ReconstituitionHumanThymus

[ofanobilbao]

Project short name:

ReconstituitionHumanThymus

Primary Wrangler:

Ami

Secondary Wrangler:

Associated files

• Google Drive: folder sheet

Link to Ingest

• https://contribute.data.humancellatlas.org/projects/detail?uuid=3e92c74d-256c-40cd-9273-16f155da8342

Published study links

• Paper: Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds

• Accessioned data: GSE159745

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
• [ ] 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

[ami-day]

Almost done curating. Requested NCBI Cloud Delivery of fastq files.

[ami-day]

Submitted new HCA ontology request for cell type ontologies: "stromal cell of thymus" and "interstitial cell of thymus"

[ami-day]

Requires some info. from authors

[Wkt8]

Assigning self for secondary-review

[Wkt8]

Project tab:

• I don't think the cell count of 51600 is right in the project level metadata. Do you have a better idea of what it might be?

Donor_Organism:

• You currently have 8 donor organisms for the GEO dataset, 2 donor organisms for each sample. I think these may be duplicates and there was only one donor for the GEO dataset (scRNA-seq)
• What evidence do you have that each of the GEO samples originated from a separate donor? It seems like they all come from a 6 month old healthy female and each of the different samples is a different cell subpopulation
  • e.g. Type1 mTEC, Type 1 cTEC, Type 2 mTEC, Type 2 cTEC
• You could also add the gender (female) and age (6 months) metadata

Cell_Suspension

• missing the thymic interstitial cell type ontology term. I had a look at 'Interstitial cell' is available but might not be specific enough. Do you want to request a new ontology term?
• Could also add cortical thymic epithelial cell and medullary thymic epithelial cell to the scRNA-seq cell suspensions

Sequence_File

• Could not really check these as they don't have the appropriate file names at the moment
• Looking at the SRA run selector it looks like the fastqs are available though, which is great!

Analysis Protocol

• Ontology term and ontology term labels missing from analysis_protocol.type

[ami-day]

• missing the thymic interstitial cell type ontology term. I had a look at 'Interstitial cell' is available but might not be specific enough. Do you want to request a new ontology term?

Thanks @Wkt8 , working on these updates now. I had requested a new cell type ontoology term for "interstitial cell of thymus" and also "stromal cell of thymus" above it, so they will need to become available before I submit.

[ami-day]

Downloading data files

[ami-day]

bf632dd7-a33a-446c-b3e5-193f27abc05a

[ami-day]

We are waiting on the new cell type to be added to HCAO.

Message from Zoe: Bradley has closed the ticket as he has added the requested terms to CL. After CL has it’s next release we will then be able to import these into HCAO and they’ll be available to you following that HCAO release. As CL is not under my control I can’t predict when the next release will be to give you a timeline for these terms being in HCAO.

I will move forward with this project using "stromal cell" as the cell type, and then update the project with the precise cell type ontology "interstitial cell of thymus" when it becomes available.

[ami-day]

synced files

[ami-day]

Graph validating

[ami-day]

Submitted.

[ami-day]

Exported, submitted import form.

[ami-day]

Looks fine in data browser.

[idazucchi]

Missing fastq files While cleaning up the hca-util areas I noticed this project had a different number of fastq files in the hca-util area from what is available in ingest. No explanation is given in here to indicate why the files are not included in the project.

3 files are missing for accession SRP287966 - run SRR12857069 is missing)

Action I'm updating the accession with the missing files

[idazucchi]

tried to export project but spreadsheet generation fails due to sequence_file schema version error

{"log":"2023-08-03 10:56:23,020 - TerraSpreadsheetExporter - ERROR - submission_uuid:d1ce4d66-ad64-4a4d-9ac6-cd1eabc0aa20 - export_job_id:64cb879b1bfdb743144de671 - project_uuid:3e92c74d-256c-40cd-9273-16f155da8342 - The concrete entity schema version should be consistent across entities. Multiple versions of same concrete entity schema found: ['https://schema.humancellatlas.org/type/file/9.4.0/sequence_file', 'https://schema.humancellatlas.org/type/file/9.5.0/sequence_file']\n","stream":"stderr","time":"2023-08-03T10:56:23.02120782Z"}

• Amnon changed status so Ida can edit the metadata and update schema to 9.5.0

[idazucchi]

I've update the schema version to 9.5.0 for all sequence_file, exported and filled out the import form

[idazucchi]

all the new files made to the browser as well as the spreadsheet