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
Common Data Templates for MODEL-AD
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
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
JAX | IU | PITT | UCI | ||
DMP | DMP | PTC | PTC | DMP | |
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)
Clinical – Blood chemistry measurement
Metadata
No metadata template.
Data
Electrophysiology – LTP
Metadata
No metadata template.
Data
No data template.
Gene Expression – mRNA counts (Nanostring)
Metadata
Data
No data template. Provide raw files and processed file.
Gene Expression – RNAseq
Metadata
Data
No data template. Provide fastq files and counts only; do not include BAM files.
Imaging – Autorad
Metadata
Data
No data template.
Imaging – MRI
Metadata
Data
No data template.
Imaging – PET
Metadata
Data
No data template.
Immunoassay – Electrochemiluminescence
Metadata
No metadata template
Data
Immunoassay – Immunofluorescence
Metadata
No metadata template.
Data
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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