RatGTEx Portal

This portal provides gene expression, eQTL, and sQTL data for multiple rat tissues. It is managed by the NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844).



The raw data for the tissues in this portal come from multiple studies. The processed data, however, may differ from the results reported in each study for a couple reasons:

  1. Different processing decisions could be made for each study, while the data in this portal are processed uniformly to facilitate comparison across tissues.
  2. The published study results are immutable, while new versions of data in this portal may be released, for example to improve quality or to use updated reference genome and annotations.
Nevertheless, we also host the original results from individual studies on the Download page when available.

Sample sizes for rn6 and rn7 versions differ due to availability of genotypes and filtering of mismatched genotype/RNA-seq samples.
TissueAbbreviationSamples (rn6)Samples (rn7)Originating study
Infralimbic cortexIL8183P50 DA037844 Y1-5, Project 2
Lateral habenulaLHb8182P50 DA037844 Y1-5, Project 2
Nucleus accumbens coreNAcc7577P50 DA037844 Y1-5, Project 2
Orbitofrontal cortexOFC8082P50 DA037844 Y1-5, Project 2
Prelimbic cortexPL8082P50 DA037844 Y1-5, Project 2
EyeEye5153R01 EY021200
Basolateral amygdalaBLA185191U01DA046077
Nucleus accumbens coreNAcc2188193U01DA046077
Prelimbic cortexPL2191194U01DA046077
Brain hemisphereBrain339340Pilot: Creating the dataset for TWAS in HS rats

Data Use

For the tissues above whose originating study has been published (see below), you may use the data in your studies by citing the originating study. For the other tissues, contact us about whether, when, and how you may use them.

Associated Studies

More info on the ratgenes.org eQTL page. Additional publications will be posted when available.

Tissues from the same study are from the same set of rats, though the final subsets per tissue differ slightly after quality control filtering. See the sample info page for details.

P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
R01 EY021200: Genetic Modulators of Glaucoma
U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model
R01DK106386: Systems genetics of adiposity traits in outbred rats
Pilot: Creating the dataset for TWAS in HS rats


Also try searching for a gene in the toolbar to view its expression and eQTLs.


For questions or comments related to the data or website, email Daniel Munro at dmunro@health.ucsd.edu.

RatGTEx is primarily developed in the labs of Abraham Palmer at UC San Diego and Pejman Mohammadi at Seattle Children's Research Institute and University of Washington.


RatGTEx is produced by the NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844). It is not a project of the GTEx Consortium.

Code for visualizations was adapted from the GTEx portal viz tools, and additional design considerations were inspired by the GTEx portal.