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This page describes how MODEL-AD teams should contribute new mouse data to the AD Data Coordination Center (AD-DCC).

An overview of the data contribution steps can be found in the AD Knowledge Portal Docs.

Planning

In our data uploading onboarding call, we will review how MODEL-AD content is organized by Study in the portal and how files must be structured before transfer. The Data Liaison, Data Uploader, and Curator will coordinated to to understand precisely what content will be transferred (data type, file format, file naming, number of files).

Let us know about your next planned data contribution: https://forms.gle/YJaPuEumYRnwm8916

The Curator will create the Study in Synapse with a directory structure that is appropriate for the data types including a private Staging directory for data uploads. SynapseIDs for the metadata and data staging locations will be provided for your file transfer.

Data Templates

All available data templates

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Data Templates

Each template should also include a Data Dictionary with a list of each key-definition pair. Each data template should have a brief Assay description (3-5 sentences) about data collection.

See all the available data templates

MODEL-AD Data Templates

• Immunofluorescence

  • abeta_molecular

  • immunofluorescence

  • pathology

• Long-term Potentiation

  • LTPIOCurve

  • LTPPPF

  • LTPSlopeExp

...

Assay Description

Each data template should have a brief description (3-5 sentences) about the procedures for data collection. This information will be posted on the file wiki.

Data Dictionary

Each template should also include a definition of each variable name. This will include a list of each key-definition pair in a data dictionary worksheet.

Examples

• Immunoassay Templates

  • Pathology

    • Template mockup in development with UCI

    • General Description:

    • Key-Definition Pairs:

    • Link to the final template in Synapse:

  • Immunofluorescence

  • ABeta Molecular

  • Proinflammatory Molecular

Data Type

• File naming:

• Assay metadata template:

• Data template:

...

MODEL-AD Data Collection across Sites

Behavior Process

• Metadata

  • No metadata template

• Data

  • Elevated + maze data template (pending)

  • Frailty assessment data template (see stand-alone frailty assessment data dictionary)

  • Open field data template (see stand-alone open field data dictionary)

  • Rotarod data template

  • Spontaneous alternation data template

  • Wheel running data template

Clinical – Blood chemistry measurement

• Metadata

  • No metadata template.

• Data

  • Blood chemistry measurement data template

Electrophysiology – LTP

• Metadata

  • No metadata template.

• Data

  • No data template.

Gene Expression – mRNA counts (Nanostring)

• Metadata

  • Nanostring metadata template

• Data

  • No data template.  Provide raw files and processed file.

Gene Expression – RNAseq

• Metadata

  • RNAseq metadata template  

• Data

  • No data template.  Provide fastq files and counts only; do not include BAM files.

Imaging – Autorad

• Metadata

  • Autorad metadata template

• Data

  • No data template.

Imaging – MRI

• Metadata

  • MRI metadata template

• Data

  • No data template.

Imaging – PET

• Metadata

  • PET metadata template

• Data

  • No data template.

Immunoassay – Electrochemiluminescence

• Metadata

  • No metadata template

• Data

  • Proinflammatory data template

  • Abeta data template

Immunoassay – Immunofluorescence

• Metadata

  • No metadata template.

• Data

  • Immunofluorescence data template

Immunoassay – Western blot

• Metadata

  • No metadata template.

• Data

  • No data template.

Pharmacokinetic Study

• Metadata

  • No metadata template

• Data

  • No data template. 

  • Each set of output should be its own CSV file.  The header of each file should only be one row – values and their units should not be in separate cells.

Data Transfer

This section describes how MODEL-AD teams should contribute data to the DCC. In our onboarding call, we will review how MODEL-AD content is organized in the portal. It is important we all understand clearly what content will be transferred (data type, file format, file naming, number of files).

Let us know about your next planned data contribution: https://forms.gle/YJaPuEumYRnwm8916

The Curator will create the Synapse directory structure that is appropriate for the data types including a private staging directory for data uploads. The SynapseIDs for the staging directories will be provided.