BALPreschoolCF

[idazucchi]

Project short name:

BALPreschoolCF

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes

• Accessioned data: zenodo

• Ingest

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
• [x] Submit dataset to Production
• [x] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

the metadata for the donors is in the supplementary pdf --> copied here in xlxs

the analysis files come from https://oshlacklab.com/paed-cf-cite-seq/

[Wkt8]

Hey! Looks good, well done!

Ingest

• I added CITE-seq to the project techniques

Project Tab

• The word 'abstract' in the project description could be removed

Enrichment_Protocol

• A lot of the chemical things here are missed out (the sample being resuspended in media and chilled freezing solution, etc. how the cryopreserved BAL was thawed)

Library_Preparation_Protocol

• Looks good! I wasn't sure where you found the information about the umi_barcode offset, etc. for the CITE-seq technique though. Should we addd it to the online excel sheet? (https://docs.google.com/spreadsheets/d/1H9i1BK-VOXtMgGVv8LJZZZ9rbTG4XCQTBRxErdqMvWk/edit#gid=0)

Analysis_File

• Cell_Count of the analysis_Files is really high considering the project cell count is 42,658
• One of the files is p13 but the other one is not (10X) for Patch version.

[idazucchi]

Applied corrections, exported and filled out the import form

[idazucchi]

Verified in Data Browser