GSE145926 - Covid19BALFLandscape

[arschat]

Project short name: Covid19BALFLandscape

Primary Wrangler:

Arsenios

Secondary Wrangler:

Ida

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

• Accessioned data: GSE145926

• ingest: 08fb10df-32e5-456c-9882-e33fcd49077a

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] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [x] Upload sheet to validate metadata
• [x] Transfer raw files to ingest to validate data files
• [x] Check linking using ingest graph validator
• [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

[arschat]

RDS analysis file, includes data from another publicly available dataset (here), but not wrangled in DCP & not eligible.

I will try to find metadata from specific donor and include in spreadsheet.

[arschat]

No metadata available for the extra donor. Used a dummy donor/specimen & CS for this.

There is ambiguity about the sequence machine used.

The constructed library was sequenced on a BGI MGISEQ-2000 or Illumina platform.

In GEO, only BGI is mentioned, however it is not in the EFO ontology for high throughput sequencers. It exists in the GENEPIO ontology http://purl.obolibrary.org/obo/GENEPIO_0100144.

An ontology request should be made.

[arschat]

CellxGene wrangling requirements

• [X] Raw count matrix: nCoV.rds
• [X] Normalised count matrix: nCoV.rds
• [X] cell type annotations (cell type linked to barcode): github
• [ ] ENSEMBL ID of genes: MISSING
• [X] x-y coordinates (tsne, umap, pca): nCoV.rds

(genes are in gene symbol format in the count matrices)

[arschat]

Ontology request needed, leave for next release.

[arschat]

Ontology request made but even if new term is added, OLS update should be made to proceed.

[arschat]

Ontology term added, will be available in EFO in next release. BGI MGISEQ-2000 -> EFO:0700018

[idazucchi]

this dataset is potentially affected by the deletion of data from ncbi-cloud-data bucket - can you check @arschat ?

[arschat]

Files had already been uploaded in the hca-util area 9d41ab58-c57d-4804-926f-3d63275ed913

[arschat]

Will try to push project despite the ontology stalled.

• Sent email to authors to verify that BGI MGISEQ-2000 is the sequencer used.
• Option to add high throughput sequencer temporarily until the ontology is pushed.

[arschat]

Authors replied:

We use BGISEQ-500 to sew.

Therefore we should proceed with the other option.

[arschat]

Uploaded file with swapped the insdc_project_accession and insdc_study_accession but fix that with the following code through api:

from hca_ingest.api.ingestapi import IngestApi token = "" api = IngestApi(url="https://api.ingest.archive.data.humancellatlas.org/") api.set_token(token) project_url = "https://api.ingest.archive.data.humancellatlas.org/projects/60068ceec9762f5f0de9f719" headers_json = {'Content-Type': 'application/json', 'Authorization': 'Bearer ' + token} results = api.get(project_url).json() results['content']['insdc_project_accessions'] = ['SRP281979'] results['content']['insdc_study_accessions'] = ['PRJNA662785'] api.put(project_url, headers=headers_json, json=results)

Seems correct in ingest now.

Waiting for files transfer and if graph valid, it will be ready for secondary review.

[arschat]

Some files in upload-area seems to be invalid, size for some fastq.gz files does not match the size mentioned in ncbi probably duplicated R1 to R2 of same library. I requested a new ncbi cloud transfer.

[arschat]

Downloaded SRA Lite fastqs instead of original files. If I redownload the correct files, I will surpass my monthly limit. Will ask other wrangler to download through their account these SRA files.

[arschat]

Thanks to Ida, correct files have been downloaded.

• [X] move files to hca-util upload area
• [X] sync files to hca prod area

[arschat]

re-triggered validation using script here, seems stuck in same file (C51_R2.fastq.gz)

[arschat]

Deleted submission & re-submit.

• [x] Metadata valid
• [x] Graph valid Ready for sec review

[idazucchi]

Nice job! I have a few suggestions for information you can add

Project

you can add the visualisation portal to the supplementary links

Donor

• healthy controls can be marked as disease normal
• you can add to the description the disease outcome
• you can also fill in the timecourse with the disease duration

Specimen

• healthy controls can be marked as disease normal
• you can remove the disease from the adjacent diseases - it's intended for use with topical diseases, like tumors or lesions, and the systemic diseases are already recorded at the donor level
• for preservation method it sounds to me like the samples were processed fresh

  Approximately 20 ml of BALF was obtained and placed on ice. BALF was processed within 2 h and all operations were performed in a BSL-3 laboratory.

• you can add the time of collection for the BALF and the timecourse for the time elapsed between the symptoms onset and the sampling (or the hospitalisation)

CS

• one cell suspension per library - nice - I'm still getting used to it

Sequence file

• you could compress the fastq files

Analysis protocol

• can remove gene filtering, cell filtering and doublet removal from raw_matrix_generation

Analysis files

• can we make sure we're all using gene expression / count matrix as raw/processed? maybe we can raise this at the next wrangler call
• do we have a better term to describe TCR files rather than sample annotation? maybe we need to request one

[arschat]

About fastq compressing. Data files were very large (~4 TB) and have been transferred through s3 buckets (ncbi to hca-util to upload-prod), and therefore in order to be compressed should be downloaded locally or on EC2, compressed and re-uploaded which would take a lot of time. Since there were also previous problems with the file validation, I didn't want to play too much with those. For those reasons I skipped the fastq compression.

All other changes were submitted (Donor timecourse -> Symptoms to Outcome/ Specimen timecourse -> Symptoms to Sampling date). Did not found other term for TCR files.

Submission is now on Submitted state and I when it will be exported I will sent the import form.

[arschat]

Verified in browser, however, sequencing_protocol.instrument_manufacturer_model needs update when a new OLS is available. BGI MGISEQ-2000 -> EFO:0700018

[arschat]

Since ols update is completed, we can now add the correct sequencer information.

[arschat]

• [x] Added correct sequencer of protocol through the UI
• [x] metadata & graph valid
• [x] export metadata
• [x] import form sent