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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).

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All available data templates

Common Data Templates for MODEL-AD

• Immunofluorescence

  • abeta_molecular

  • immunofluorescence

  • pathology

• Long-term Potentiation

  • LTPIOCurve

  • LTPPPF

  • LTPSlopeExp

• Behavioral

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:

Data Types Collected at 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.

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