GSE280502 - AirLiquidInterfaceLungOrganoids

[arschat]

Communications

Project short name:

AirLiquidInterfaceLungOrganoids

Primary Wrangler:

Secondary Wrangler:

Associated files:

• Google Drive:
• accessions: GSE280502
• publication: 10.3390/cells13231991 - Transcriptomic Analysis of Air–Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial Differentiation
• ingest: 4ac19826-264b-4e64-bf38-f800e83cc067

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.

[arschat]

Once T&C is accepted we will share the spreadsheet for organoids and I would like to make a graph with mermaid to help them understand the experimental graph they've used.

[arschat]

flowchart TD
    al(["Donor organism"])
    bi(["Specimen from Organism"])
    ca(["Cell suspension"])
    ep(["Organoid"])
    fi(["Sequence file"])
    ga(["Analysis file"])
    al -- Collection protocol -->  bi
    bi -- Dissociation protocol --> ep
    ep -- Dissociation protocol --> ca
    ca -- Sequencing protocol/ Library preparation protocol --> fi
    ca -- Sequencing protocol/ Library preparation protocol/ Analysis protocol --> ga

    A(["Donor organism"])
    B(["Specimen from Organism"])
    C(["Cell suspension"])
    D(["Cell line"])
    E(["Organoid"])
    F(["Sequence file"])
    G(["Analysis file"])
    A -- Collection protocol -->  B
    B -- Dissociation protocol --> D
    D -- Differentiation protocol --> E
    E -- Dissociation protocol --> C
    C -- Sequencing protocol/ Library preparation protocol --> F
    C -- Sequencing protocol/ Library preparation protocol/ Analysis protocol --> G

    a(["Donor organism"])
    b(["Specimen from Organism"])
    c(["Cell suspension"])
    e(["Organoid"])
    ed(["Organoid"])
    f(["Sequence file"])
    g(["Analysis file"])
    a -- Collection protocol -->  b
    b -- Dissociation protocol --> e
    e -- Differentiation protocol --> ed
    e -- Dissociation protocol --> c
    ed -- Dissociation protocol --> c
    c -- Sequencing protocol/ Library preparation protocol --> f
    c -- Sequencing protocol/ Library preparation protocol/ Analysis protocol --> g

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merged

flowchart TD
    A(["Donor organism"])
    B(["Specimen from Organism"])
    C(["Cell suspension"])
    D(["Cell line"])
    E(["Organoid"])
    Ee(["Organoid"])
    F(["Sequence file"])
    G(["Analysis file"])
    A -- Collection protocol -->  B
    B -- Dissociation protocol --> D
    D -- Differentiation protocol --> E
    E -- Dissociation protocol --> C
    B -- Dissociation protocol --> Ee
    Ee -- Differentiation protocol --> E
    C -- Sequencing protocol/ Library preparation protocol --> F
    C -- Sequencing protocol/ Library preparation protocol/ Analysis protocol --> G
    B -- Dissociation protocol --> E

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[arschat]

Credentials sent to contributor's email #1338