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).

Tissues

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.

Tissue	Abbreviation	Samples (rn6)	Samples (rn7)	Originating study
Infralimbic cortex	IL	81	83	P50 DA037844 Y1-5, Project 2
Lateral habenula	LHb	81	82	P50 DA037844 Y1-5, Project 2
Nucleus accumbens core	NAcc	75	77	P50 DA037844 Y1-5, Project 2
Orbitofrontal cortex	OFC	80	82	P50 DA037844 Y1-5, Project 2
Prelimbic cortex	PL	80	82	P50 DA037844 Y1-5, Project 2
Eye	Eye	51	53	R01 EY021200
Basolateral amygdala	BLA	185	191	U01DA046077
Nucleus accumbens core	NAcc2	188	193	U01DA046077
Prelimbic cortex	PL2	191	194	U01DA046077
Adipose	Adipose	411	411	R01DK106386
Liver	Liver	401	411	R01DK106386
Brain hemisphere	Brain	339	340	Pilot: 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

• 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

R01 EY021200: 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

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.