Data Sharing
The PARC data sharing plan comprises several related efforts:
1. 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
2. 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.
3. 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 - see below
Alcohol Behavior Related Quantitative Trait Loci (QTLs) Data Set
B6D2 F2 Whole Brain Gene Expression Data
BXD RI Data Set
Inbred Strains Data Set
Alcohol Behavior Related Quantitative Trait Loci (QTLs) Data Set
The QTL data are organized into a set of three downloadable PDF documents:
1. View details of individual QTLs - AlcoholQTLsDescriptions
2. View QTLs by chromosome - AlcoholQTLsByChromosome
3. View QTLs by phenotype - AlcoholQTLsByPhenotype
Notes:
We thank Beth Bennett for updated LOR data.
This data set is also available as an Excel spreadsheet, upon request.
Contact Mark Rutledge-Gorman 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 upon request. Please contact Mark Rutledge-Gorman.
BXD RI Data Set
The Portland BXD RI data set can be downloaded as an Excel spreadsheet here.
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. To access the larger data set, go to NerveNet.org, scroll down and click on "BXD Phenotype Database."
Inbred Strains Data Set
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 Mark Rutledge-Gorman for data or more information.