This portal provides gene expression, eQTL, and sQTL data for multiple rat tissues. It is managed by the NIDA Center of Excellence for Genetics, Genomics, and Epigenetics of Substance Use Disorders in Outbred Rats (P30DA060810).

Data Release v3

The data and visualizations on this site are for the RatGTEx v3 release. The main changes from v2 are:

• Four tissue datasets from two new projects have been added, including two new brain regions, posterior ventral tegmental area (pVTA) and rostral medial tegmental nucleus (RMTg).
• Samples of the same tissue from different projects are now analyzed as a single dataset, increasing the sample size and statistical power for eQTL mapping.
• The rn7 (mRatBN7.2) genome assembly is still used, but RefSeq gene annotations are now used instead of Ensembl.
• Genotype data for all tissues have been updated.

The previous versions using rn6 and rn7 are now referred to as v1 and v2, respectively, and are still available from the Download page.

Tissues

Sample sizes reflect the final post-QC datasets.

Tissue	Abbreviation	Samples	Originating studies (see below)
Adipose	Adipose	411	R01DK106386
Basolateral amygdala	BLA	191	U01DA046077
Brain hemisphere	Brain	341	Pilot: Creating the dataset for TWAS in HS rats
Eye	Eye	53	R01EY021200
Infralimbic cortex	IL	83	P50DA037844 Y1-5
Lateral habenula	LHb	82	P50DA037844 Y1-5
Liver	Liver	411	R01DK106386
Nucleus accumbens core	NAcc	430	P50DA037844 Y1-5, U01DA046077, P50DA037844 Y5-10
Orbitofrontal cortex	OFC	82	P50DA037844 Y1-5
Prelimbic cortex	PL	407	P50DA037844 Y1-5, U01DA046077, P50DA037844 Y5-10
Posterior ventral tegmental area	pVTA	153	P50DA037844 Y5-10
Rostromedial tegmental nucleus	RMTg	93	U01DA044468

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

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.

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

P50DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration

• Publication: The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats
• Investigator: Hao Chen, UTHSC
• Prior experience/treatment: Naive
• Sex ratio: 43 Female, 45 Male
• Age: Mean 86.3 days, SD 3.1

R01EY021200: Genetic Modulators of Glaucoma

• Publication: Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats
• Investigator: Monica Jablonsky, UTHSC
• Sex ratio: 29 Female, 24 Male

U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model

• Investigators: Suzanne Mitchell and Robert Hitzemann, OSHU
• Prior experience/treatment: Behavior testing - delay discounting
• Sex ratio: 100 Female, 100 Male

R01DK106386: Systems genetics of adiposity traits in outbred rats

• Publication: Genetic mapping of multiple traits identifies novel genes for adiposity, lipids, and insulin secretory capacity in outbred rats
• Investigator: Leah Solberg Woods, WFU
• Prior experience/treatment: Naive, normal diet
• Sex ratio: All male
• Age: 17 weeks

Pilot: Creating the dataset for TWAS in HS rats

• Investigator: Francesca Telese, UCSD
• Prior experience/treatment: Naive
• Sex ratio: 176 Female, 168 Male

U01DA044468: Genomic analysis of avoidance learning in addiction

• Investigator: Tom Jhou, University of Maryland
• Prior experience/treatment: Extreme high and low phenotypes in cocaine-avoidance and punishment resistance
• Sex ratio: 48 Female, 45 Male

P50DA037844 Y5-10, Project 2: Socially-acquired nicotine self-administration

• Investigator: Hao Chen, UTHSC
• Prior experience/treatment: Naive
• Sex ratio: 84 Female, 81 Male

Visualizations

• Expression Heatmap for top expressed genes
• Expression Heatmap for a query gene list
• eQTL Dashboard
• Gene-eQTL Visualizer

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

Contact

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.

Acknowledgments

RatGTEx is produced by the NIDA Center of Excellence for Genetics, Genomics, and Epigenetics of Substance Use Disorders in Outbred Rats (P30DA060810). 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.

More info

RRID:SCR_022145

See also PhenoGen Informatics, the site for quantitative genetics of the transcriptome.