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Table of Contents

Documentation for how to provide information about new strains

This article This page describes the process procedure for how the MODEL-AD teams submit new strain information. This information should submit mouse models to the DCC. The mouse models will be posted as on the experimental tools page on the AD Knowledge Portal’s Data Coordination Center (AD-DCC)Portal.

Step 1:

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Strain Information to include

Each strain should include the key details listed below. The model details should match the information on the Jax strain webpage, and any discrepancies will need to be resolved.

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Submit Mouse Model details

Please provide information about the mouse model in this MODEL-AD Tools survey. The strain information should match that on the JAX stock page.

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  • Email address of the person submitting the survey

  • MODEL-AD Grant number

  • Species

  • Model Common Name as used in the strain list on the MODEL-AD Strain Tablesystem name (see names in the AD Metadata Dictionary)

  • Model URL (link to Jax strain page – eg, stock page (ex: https://www.jax.org/strain/031988)

  • Report card URL (link to AlzForum research model , if available(ex: https://www.alzforum.org/research-models/3xtg)

  • Model description (<500 characters)Targeted

  • GenesList of genes the model is targeting

  • Background strain (eg, C57BL/6J)

  • Type (LOAD – Late Onset Alzheimer’s Disease, FAD – Familial Alzheimer’s Disease)

Add Model to Synapse

Create Model Entity in Synapse

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Step 2: Model added to the Portal

The DCC creates a new entity in Synapse’s Experimental Tools for your model. The Synapse entity will be named after the Model Common Name and will link to the Jax lab stock page.

  1. Navigate to AD Knowledge Portal’s Experimental Tools page

  2. Click Folder Tools > Add New Folder

  3. Name the folder with the Model Common Name

  4. Add a URL to the Jackson labs strain (eg, https://www.jax.org/strain/123456)

Annotate Model

The AD-DCC will then annotate the model entity further with the content provided in the survey.

  1. Navigate to the Experimental Tools file view

  2. Download the Experimental Tool

    1. Click Download Options > Export Table

    2. Click Download as CSV

  3. Add annotations to CSV file using a text editor or spreadsheet software

  4. Upload your revised CSV to the entity view to populate annotations

Link to Experimental Tool

The AD-DCC create a link to any study that includes data from the model.

This is a Synapse file view that includes a query for all data associated with the model and is not limited to individual studies.

MODEL-AD teams provide mouse model reports

MODEL-AD teams should provide a mouse model report in PDF format.

The MODEL-AD data liaison should provide the AD-DCC with this report somehow and at some interval….

Test and see if Google forms allows for attachments. We could capture the report at the same time.

The Sage DCC will add the mouse model report into System Name. This entity will be annotated with the information provided, including a link to the JAX stock page, and a list of studies that include data from the model.

The DCC will add the PDF report to the Mouse Model Reports in Synapse.

AD-DCC sets necessary sharing permissions

Since the mouse model reports do not include sensitive information or PII/PHI, they are eligible for anonymous viewing and download permissions in Synapse. The Sage Governance team is responsible for enabling sharing permissions for each file in Synapse.

To set permissions the DCC curator must:

  • Create a Jira ticket and assign to Director.

  • The director will assign Jira ticket to the Sage Governance team.

  • Governance will set permissions as needed at the file level.

Sage DCC updates file view with link to model report

Sage DCC updates file view with a link to the mouse model report in the Experimental Tools

Create and share Model release notes

The AD-DCC writes release notes to inform the community that

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Step 3: Community Update

The DCC informs the community when a new model is available . The release notes will link to the Experimental Model card on the Portal in the AD Knowledge portal.

Past release notes are available in this document.

Zoe posts release notes in news section of portal.

When new model available should create a feature story about model in newsletter (**Discuss this option w/ MODEL-AD teams**)

News stories Portal News. See past Public Data Release Notes.