E-MTAB-11528 - LungOrganoidsTCR

[arschat]

Project short name: LungOrganoidsTCR

Primary Wrangler:

Arsenios

Secondary Wrangler:

Wei

Associated files

• Google Drive: folder

Published study links

• Paper: biorxiv

• Accessioned data: E-MTAB-11528

• ingest: 37e0f3d3-bf2a-4511-9696-322d5abd6395

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
• [ ] 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]

Communication with contributor Peng He here

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Will help Peng He with the BioStudies submission of new organoid data. Meanwhile I will wrangle both archived and the organoid metadata.

[arschat]

Archived data has been wrangled. Metadata valid & files are re-transfered to see if graph valid (there was a corrupted fastq file).

Asked for update from Peng He on the organoid data. We have to decide if we will submit the archive dataset on a different submission from the organoid dataset as an experiment for multiple submissions for each dataset of a project.

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Graph valid, no reply from Peng.

We have to decide if we will submit the archived dataset on a different submission from the organoid dataset as an experiment for multiple submissions for each dataset of a project.

[arschat]

Peng replied that they are still working on it, filling the hca spreadsheet.

[Wkt8]

Assigning for secondary review.

[Wkt8]

Secondary Review comments Project

• should the cell_count not be 61,757 cells because 77,559 is after it is combined with the previous whole fetal lung scRNAseq data?

Donor_Organism

• For the pooled samples, how did you determine the sex of the samples? Some of them are listed as 'unknown', is this why? (e.g. HDBR15084)

Specimen_From_Organism

• It's interesting here! Obviously each of the samples has a separate BioSamples accession, but also I'm not sure if it's the most accurate way to model them by pooling the samples at this stage. What do you think of having an individual sample per donor and pooling in the cell_suspension stage?
• Unless, of course, there are multiple separate pooled samples from the donors! That would make sense with the way it has been modelled in the .sdrf.

Library_preparation_protocol

• I'm not sure about the 'cell_barcode' length for the 10x_tcr_lib_prep - should it not be also 16 bp?

Sequencing_protocol

• Sequencing protocol description says it's a NovaSeq 600, but it should be a NovaSeq 6000?

[arschat]

• About pooled samples' sex, although the sex is filled in all samples, there is some inconsistency between samples from the same donor i.e. HDBR14732 has been used in two samples. In the individual sample (FL1) it is referenced as male, but the pooled sample with other donors (FL15), it is referenced as female. More on the second spreadsheet of this metadata excel file. Since it is mentioned that

  karyotype analysis was undertaken on every sample by HDBR

  we could ask the authors for more clarification on this. Update: Peng replied with the correct mapping.

• About specimen_from_organism modelling, I was focused into capturing the sample_ID as the authors provide it at the specimen level. In order to keep the information of the experimental design but also capture the author provided sample_ID at the specimen level, I remodeled the project with sample_ID with donor_ID surfix for the pooled specimens but also author provided sample_ID in the biomaterial_name field.

Next tasks:

• [X] graph valid
• [ ] Decide if we will proceed with 2 submissions
  • [ ] Submit this submission
• [ ] Wrangle organoid data

[arschat]

Peng updated with spreadsheet here.

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Organoid fastq & all processed files provided for AE update. Manuscript is now published on peer-reviewed journal here.

Since processed and fastsq files were submitted to AE we did not have access to download them. Therefore, we have to wait for the AE update before we update in DCP.

[arschat]

Updated spreadsheet is in google drive, and waiting for publication of AE submission, so we can download files from there.

There is a problem, since in the experimental design for organoids the treatment protocol is used. However, at the moment treatment protocol cannot be imported from broad (see conversation here).

As a temporary solution, we can model it as a differentiation protocol, however that would not be accurate.

[arschat]

Decided to put on hold until broad import treatment bug is fixed.

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Treatment protocol errors first occurred in #856