Project Completion QA Checklist: Mouse Endoderm Project

[jychien]

Project UUID: 4e6f083b-5b9a-4393-9890-2a83da8188f1 Project Title: The emergent landscape of the mouse gut endoderm at single-cell resolution Project Short Name: Mouse Endoderm Project Submission UUID: 0fb44736-c50f-49ab-bcdc-0985e596b955 Environment: Production

"Mouse Endoderm Project" needs to be re-ingested to correct linking of specimen to cell suspension. Go through Project Completion QA Checklist prior to re-ingest into production.

• [x] Process QA of primary bundles
• [x] Metadata tsv validation: Run metadatatsv_validator.py

[jahilton]

Findings from tsv validation

• collection_protocol.protocol_core.publication_doi:https://doi.org/10.1002/dvdy.20843 does not match pattern (most dois do not have the 'https://doi.org/')
• library_preparation_protocol.cdna_library_amplification_method.text:PCR entered but not library_preparation_protocol.cdna_library_amplification_method.ontology
• library_preparation_protocol.library_construction_method.ontology_label:10X v2 sequencing but sequencing_protocol.paired_end:True should be False
• project.insdc_project_accessions:SRP171152 & project.insdc_study_accessions:PRJNA507618 do not match pattern - likely swapped
• library_preparation_protocol.library_construction_method.ontology_label:10X v2 sequencing needs to be updated to 3' or 5' term
• organ_parts.ontology: UBERON:0003257 [yolk sac endoderm] & UBERON:0008800 [parietal endoderm] are not descendants of organ.ontology:UBERON:0000925 [endoderm]

These have been added to https://github.com/HumanCellAtlas/hca-data-wrangling/issues/365

Also, library_preparation_protocol.input_nucleic_acid_molecule.ontology:OBI:0000869 is polyA RNA extract but input as polyA RNA Mentioned first in HumanCellAtlas/hca-data-wrangling#130. It is a consistent issue across submissions. So it should stay as it is unless a large-scale decision is made to change.

[jahilton]

I'll also note that the sequencing files are all format:fastq.gz but should be fastq. Being discussed in https://github.com/HumanCellAtlas/hca-data-wrangling/issues/127

[jychien]

Process QA found the following issues:

1. Specimen e5.5_whole_embryos_rep3 was not linked to a cell suspension. Already mentioned in HumanCellAtlas/hca-data-wrangling#365
2. Short name is "Mouse Endoderm Project". The short name should be machine readable and spaces should be removed. This has been added to HumanCellAtlas/hca-data-wrangling#365

[jychien]

Also saw:

3. Donor is listed as 4-6 week old female mice. Specimen are from embryo (whole embryo, endoderm and gut tube). The way it is displayed on the browser is confusing can lead to the user thinking that the specimen is from adult female mice. Not sure what the fix is, but something that would distinguish the parent female mice from the donor, which is technically embryonic mice.