MerfishCorticalLayer - Xuyu

[idazucchi]

Project short name:

MerfishCorticalLayer

Primary Wrangler:

Ida

Secondary Wrangler:

Associated files:

• Google Drive:
• Publication: Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification
• email thread here

ingest

Key Events

• [ ] Send initial instructions about contributing, including questionnaire and T&Cs
• [ ] Receive project questionnaire
• [ ] Assign the Primary Wrangler
• [ ] Receive T&C form filled out by at least 1 representative of group/project
• [ ] Send custom metadata template spreadsheet, how-to guide and directions for submitting data, matrix and cell annotation files.
• [ ] Receive spreadsheet (to a sufficient standard to submit dataset)
• [ ] Receive data, matrix and cell annotation files (to a sufficient standard to submit dataset)
• [ ] Curate metadata spreadsheet with ontologies
• [ ] Upload sheet to validate metadata
• [ ] Run graph validator & Check linking
• [ ] Validate data files
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Get final approval of submission from the contributor including release date, metadata spreadsheet and data files
• [ ] Submit to production and inform ingest-devs the project is ready for archiving
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

Please track the below as well as the key events:

1. Track date first spreadsheet received and final spreadsheet sent by editing ticket to include date next to event.
2. Track spreadsheet iterations by placing asterisks next to receive spreadsheet event.
3. Track any metadata issues/tickets made for dataset with a bulleted list of links under received spreadsheet event. Links should be to the ticket in the metadata repo.

[idazucchi]

the contributor are primarily interested in depositing Merfish data I've done a bit of research on it - this paper explains how the method works simplified explanation

We can model this with the imaging protocol + probe tab. Since the raw data is very large (160+TB) they would like to deposit processed data instead; if I understand it correctly it's something similar to a count matrix

Modeling with images

Modeling with analysis files

[idazucchi]

small hiccup with the hca-util credentials - the contributors' institution blocks emails with zipped attachments I've placed the credentials in a password protected word file instead and they are able to access them now

[idazucchi]

data: uploaded and confirmed the files are correct metadata: graph valid

release date: now discussing with contributors, I will put a reminder in my calendar to check in with them later on