PARC Data Sharing

The PARC data sharing plan comprises several related efforts:

To the extent possible, we regularly submit data to established and centralized archives according to data type.
- Inbred strains phenotypic data are submitted to the Mouse Phenome Database
- Microarray gene expression data are submitted to The Gene Network
- BXD RI phenotypic data have been submitted to NerveNet.org, and posted to WebQTL as well.
- Mouse Genome Informatics (MGI) also includes PARC data in their searchable database of mouse genes, markers, and QTLs
We continue to develop the PARCDB in-house database to integrate and store larger collections of data that will be available to PARC researchers. These data may be made available to outside investigators upon request.
We will also post additional data sets on this web site based on common requests (see below). For example, we currently maintain a list of ethanol response QTLs mapped in mice.

Available Data Sets

Alcohol QTLs

This link will take you to a list of alcohol behavior related QTLs organized by phenotype. From there you can view details on individual loci, or search by chromosome.

Notes:

Statistical and interval data were current as of 12/04.
We thank Beth Bennett for updated Lore data.
This data set is also available as an Excel spreadsheet, upon request.

Contact Michelle Bobo for more information.

B6D2 F2 Whole Brain Gene Expression Data
John Belknap and Bob Hitzemann have developed a gene expression data set from C57BL/6J x DBA/2J F2 mice (B6D2F2). Whole brain hemisphere samples were taken from 56 experimentally naive mice, with a left/right side counterbalanced design (the other half will be used later for finer dissections). Samples were run on Affymetrix 430A and 430B microarray chips, using one chip per mouse.

Analyses from this data set include eQTL mapping for all 45,000 transcripts, as well as correlation of gene coexpression. Data files, documentation, and instructions for use are available here.

BXD RI
The Portland BXD RI data set can be downloaded as an Excel spreadsheet here.
(Right-click to save the file onto your computer)

These data have also been incorporated, with data from other groups, into a larger, searchable web-accessible archive of BXD RI phenotypes at the NerveNet.org site maintained by Rob William's group at the University of Tennessee.
Click here to access the larger data set; scroll down and click on "BXD Phenotype Database."

Inbred Strains

PARC inbred strain phenotypic data is submitted to the Mouse Phenome Database and also archived in a local repository. A list of publications for which data has been submitted to MPD is available here.

The local repository contains all of the data submitted to the MPD, plus some additional as well. It represents at least 23 publications, and approximately 450 distinct variables. About 70% of that is alcohol data, including activity, withdrawal, hypothermia, BECs, and a whole range of different ataxia measures. There are also diazepam and pentobarbital data for activity and hypothermia, and a small number on other drugs. Contact Michelle Bobo for data or more information.

by Mark Rutledge-Gorman
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