GSE131907 - MetastaticLUADReprogramming

[idazucchi]

Project short name:

MetastaticLUADReprogramming

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

• Accessioned data:

  • GSE131907 matrices
  • EGAD00001005054 raw managed access data

ingest

Key Events

• Convert published metadata to HCA spreadsheet
• Manually curate dataset to meet HCA metadata standard
• 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
• Upload sheet to validate metadata
• Transfer raw files to ingest to validate data files
• Check linking using ingest graph validator
• 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

[idazucchi]

Samples
there are 58 samples in GEO, 6 more are mentioned in the paper but are not found in the data or metadata provided

A total of six tissue samples (tumor-normal pair) from three LUAD patients were additionally collected and immediately dissociated for the flow cytometry analysis. The collected tissues were as follows: LUNG_T14 (stage IIIA), LUNG_N14, LUNG_T41 (stage IIIA), LUNG_N41, LUNG_T42 (stage IA), LUNG_N42, LUNG_T43 (stage IB), LUNG_N43.

developmental stage
can we say they are all adults?

The average age was 62.2 years old

[idazucchi]

graph valid and ready for secondary review

[idazucchi]

From Wei

Your dataset looks good
I got a bit confused about the malignant plural effusion because when i looked it up it's not a technique? it's a disease or a condition? so i wasn't sure about that as a collection protocol

I also wasn't sure about using 'count matrix' as the ontology for two of the normalised analysis files but i'm not up to date about what we use nowadays

[idazucchi]

I double checked the ontology term for the pleural fluid collection protocol : there is no term specific for pleural fluid so I've used biopsy but in the free text I've left pleural effusion collection

For the count matrix - I've swapped it for Gene expression matrix

I'm exporting

[idazucchi]

import form filled