AgingSkinAtlas - A Single-Cell Transcriptomic Atlas of Human Skin Aging

[idazucchi]

Project short name:

AgingSkinAtlas

Primary Wrangler:

Ami

Secondary Wrangler:

Associated files

• Google Drive:

https://drive.google.com/drive/folders/1huwmsNCyeYSE5TzBwRPMkQw_tJVq7f17

https://docs.google.com/spreadsheets/d/12vuk9-SUKbPi4flwqi_kXmn2mBpQCSY0_SxI0AZpeEs/edit#gid=1539471600

Published study links

• Paper: A Single-Cell Transcriptomic Atlas of Human Skin Aging

• Accessioned data: HRA000395 in GSA Aging Atlas (https://bigd.big.ac.cn/aging/landscape?project=Human_Skin)

• Ingest: project

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

[ami-day]

Downloading fastq files from https://ngdc.cncb.ac.cn/aging/landscape?project=Human_Skin

[ami-day]

Note: emailed the authors about obtaining gene expression matrices files and cell type annotation files.

[ami-day]

fastq files still downloading.

[ami-day]

uploading to d0ada739-b5ca-4112-8375-c0cd24b0441b

[ami-day]

No response from authors about matrix and cell annotations files.

[ami-day]

Uploading files to hca-util bucket

[ami-day]

Graph validating.

[Wkt8]

Secondary Review: This looks great! Only two small things I wanted to check :)

Donor_Organism I couldn't find where you were getting this specific metadata for the donor_organisms - regarding the Han Chinese ethnicity, alcohol history, and smoking history?

Sequence_File Are you 100% sure that these are read1 and read2 files? Just asking as they seem to have an unusual suffix of '_f1'

[ami-day]

Secondary Review: This looks great! Only two small things I wanted to check :)

Donor_Organism I couldn't find where you were getting this specific metadata for the donor_organisms - regarding the Han Chinese ethnicity, alcohol history, and smoking history?

I found these via supplementary links via the paper and portal!

Sequence_File Are you 100% sure that these are read1 and read2 files? Just asking as they seem to have an unusual suffix of '_f1'

yep, Im pretty sure 'f1' means 'forward read 1' and then r1 means 'reverse read 1'.

[ami-day]

I will go ahead and submit it :)

[ami-day]

submitted import form, exported.