GSE114727 Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

[rays22]

Project short name:

GSE114727_BreastTumorMicroenvironment

Primary Wrangler:

Ray

Secondary Wrangler:

Enrique

Associated files

• Google Drive: https://drive.google.com/drive/folders/1WJ4dHUWMOXfskU4HU47UZwHKehufAF-o

Published study links

• Paper: Azizi E, Carr AJ, Plitas G, et al. Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Cell. 2018 Aug;174(5):1293-1308.e36. DOI: 10.1016/j.cell.2018.05.060 PMID: 29961579

• Accessioned data: GSE114727: This SuperSeries is composed of the SubSeries listed below.

  • GSE114724 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing
  • GSE114725 Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing

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] 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
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[rays22]

• I have uploaded the metadata spreadsheet to the google drive folder of the project. It is ready for secondary review.
• The project level metadata can be found in Ingest, not in the metadata spreadsheet.

[ESapenaVentura]

@rays22 I have reviewed the dataset and overall LGTM! I just have a couple of comments for some specimens:

Specimen from organism

• Changed some organs labelled with “immune organ” to “immune system” ontology
• Changed organ part for blood specimens from “peripheral blood mononuclear cell” to “venous blood” (Feels more right as an organ part, and the collection protocol does not specify any enrichment on mononuclear cells, but happy to discuss about this)

I have uploaded a reviewed spreadsheet into the folder, same name but with a ES_review appended. Let me know if you need any help checking other things or you disagree with the changes I did!

[rays22]

Thank you @ESapenaVentura for the quick review. I will implement your suggestions and then export the project.

[rays22]

I have exported the project to the DCP and filled in the data import form.