GSE207502 - MuralGingivaZhu

[arschat]

Project short name:

MuralGingivaZhu

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Mural cell composition and functional analysis in the healing process of human gingiva from periodontal intrabony defects

• Accessioned data: GSE207502

• ingest: 2433c1e4-5a12-46a5-b2d5-d3554a7694f2

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

[arschat]

hca-util upload area 4a9a1daa-578c-49ef-be4d-54b4c895028e

[arschat]

Graph valid and ready for sec review

[idazucchi]

Great work!
The only things I would suggest are

• to add something at the specimen level to describe the response to treatment, maybe in the description or gross description?
• remove matrix cell count for barcode and gene files

[arschat]

Thanksss. Applied all changes and removed the fastq generation method as well.

• graph valid
• exported
• import form sent

[arschat]

Verified in portal. Two minor updates not necessary to hold project back:

1. Arsenios Chatzigeorgiou not listed as data curator and thus listed as publication contributor
2. Bionetwork is not "Oral and Craniofacial" but "Oral & Craniofacial"
   • raised this point with Dave & execs

Since solution for 2. would be either keep the "&" as we have it now or use "and" and update schema and all ORCF projects, I will re-export this submission with metadata only to fix typo 1.

• re-export
• import form sent