Preparing and Contributing Study Documentation

If you have data you would like to contribute to the Portal, please:

Email richard.yaxley@sagebase.org with the subject: MODEL-AD - Grant# - Data Contribution
Submit the Data Contribution form with the following information:

Grant Number
Contact PIs
Study Name (see naming conventions below)
Experimental models used
Assays performed
Data Formats
Number of individuals and biospecimens collected

Study Name Conventions

MODEL-AD study names should be formatted as follows.

Study type	Naming Format	Number of Strains
Primary Screen	`Site_PrimaryScreen` Jax.IU.Pitt_PrimaryScreen UCI_PrimaryScreen	Many
Strain Validation	`Site_StrainValidation` Jax.IU.Pitt_StrainValidation UCI_StrainValidation	Many
Deep Phenotyping	`Site_Model` Jax.IU.Pitt_APOE4_Trem2 UCI_5XFAD	Many
Pharmacokinetic	`Site_Model_Drug` Jax.IU.Pitt_5XFAD_Verubecestat	One
Pilot Studies Microbiome Proteomics Metabolomics	`Site_StudyType_Pilot` Examples: Jax.IU.Pitt.Proteomics_Metabolomics_Pilot	Many

Study Organization

File Structure

Studies are organized in Synapse with a directory schema similar to this:

Study_Name/
- Data/
  - Assay_a/
  - Assay_b/
- Metadata/
- Staging/ (Note: Files will initially be uploaded to staging locations)
  - Assay_*/

File naming

File names should be concise, descriptive, and unique across the entire study. We must be able to distinguish between each file as if there were all in one directory.

See general file naming recommendations from the Princeton U Library.

Study Documentation

Each study will need a Study Description, Methods Description, and Acknowledgment Statement. The Documentation Submission Form includes some templates for these documents and instructions about submitting the documents.

Study Description

MODEL-AD specific templates are being drafted and will be made available on Synapse (see Study, Acknowledgment, and Methods). Each study should be accompanied by a brief study description that includes the species, genetic background, a link to the Jax Datasheet (if available) or a description of how the animals were created.

Methods Description

Each assay should include a brief description of the procedures, data collection, and analytical methods. This is a good opportunity to provide useful details that may not be included in the manuscript.

Acknowledgment Statement

Every MODEL-AD study should include the following acknowledgment:

The results published here are in whole or in part based on data obtained from the AD Knowledge Portal ( https://adknowledgeportal.synapse.org/ ). The IU/JAX/UCI MODEL-AD Center was established with funding from The National Institute on Aging (U54 AG054345-01 and AG054349). Aging studies are also supported by the Nathan Shock Center of Excellence in the Basic Biology of Aging (NIH P30 AG0380770).