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).
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:
- Different processing decisions could be made for each study, while the data in this portal are processed uniformly to facilitate comparison across tissues.
- 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.
| Tissue | Abbreviation | Samples | Originating study |
|---|---|---|---|
| Infralimbic cortex | IL | 81 | P50 DA037844 Y1-5, Project 2 |
| Lateral habenula | LHb | 81 | P50 DA037844 Y1-5, Project 2 |
| Nucleus accumbens core | NAcc | 75 | P50 DA037844 Y1-5, Project 2 |
| Orbitofrontal cortex | OFC | 80 | P50 DA037844 Y1-5, Project 2 |
| Prelimbic cortex | PL | 80 | P50 DA037844 Y1-5, Project 2 |
| Eye | Eye | 51 | R01 EY021200 |
| Basolateral amygdala | BLA | 185 | U01DA046077 |
| Nucleus accumbens core | NAcc2 | 188 | U01DA046077 |
| Prelimbic cortex | PL2 | 191 | U01DA046077 |
| Adipose | Adipose | 411 | R01DK106386 |
| Liver | Liver | 401 | R01DK106386 |
| Brain hemisphere | Brain | 339 | 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
- Preprint: Genome-Wide Association Study Finds Multiple Loci Associated with Intraocular Pressure in HS Rats
- Investigator: Monica Jablonsky, UTHSC
- Sex ratio: Females and Males
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
- Investigator: Leah Solberg Woods, WFU
- Prior experience/treatment: Naive
- Sex ratio: All males
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@scripps.edu.
RatGTEx is primarily developed in the labs of Abraham Palmer at UC San Diego and Pejman Mohammadi at Scripps Research.
The RatGTEx data is currently available as a beta version. Please let us know if you'd like to use it for research so we can ensure everything is correct.
Acknowledgments
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.