Several groups will collect tissue from specific brain regions. The Sequencing Core (Core C) will perform RNA-Seq on these brain regions. We will use RNA-Seq data to quantify gene expression in each brain region and use these data to map eQTLs. We will also analyze allele-specific expression (ASE) as another indicator of regulatory variation.
We have created the RatGTEx portal to provide gene expression and eQTL data for different rat tissues. The portal is available at ratgtex.org. In addition to data downloads, it has interactive visualizations that can display results for queried genes, variants, and tissues. It will specify a standard processing pipeline and data formats to facilitate comparisons across datasets.
The abundance of a gene transcript is a quantitative trait and can be mapped to genetic loci. We anticipate many of our behavioral QTL will overlap with multiple genes, while we assume only one of them is the causal gene for the trait. In these cases, the presence of an eQTL for one particular gene in the QTL region (i.e., a cis-eQTL) suggests that genetic variants regulate both the trait and the expression of that gene. It is very likely that this genetic variation regulates the behavioral phenotype by changing the expression of this particular gene (as opposed to other genes within the QTL).
Full RatGTex pipeline and protocol can be found here
Samples collected from HS rats that are available for eQTL mapping
| Project | Investigator | Tissue | N | Prior experience | Status |
|---|---|---|---|---|---|
| Pilot: Creating the dataset for TWAS in HS rats | Francesca Telese, UC San Diego | Brain: whole hemisphere | 340 | Naive | Complete, the data is in RatGTEx |
| U01DA044468: Genomic analysis of avoidance learning in addiction | Tom Jhou, University of Maryland | Brain: rostromedial tegmental nucleus | 80 | Extreme high and low phenotypes in cocaine-avoidance and punishment resistance | In progress |
| P50 DA037844 Y5-10, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: prelimbic cortex | 200 | Naive | In progress |
| U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model | Suzanne Mitchell, Robert Hitzemann, Oregon Health & Science University | Brain: prelimbic cortex | 194 | Behavior testing: Delay discounting | Complete, the data is in RatGTEx |
| P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: prelimbic cortex | 82 | Naive | Complete, the data is in RatGTEx |
| U01DA044468; Genomic analysis of avoidance learning in addiction | Tom Jhou, University of Maryland | Brain: prelimbic cortex | 80 | Extreme high and low phenotypes in cocaine-avoidance and punishment resistance | In progress |
| P50 DA037844 Y5-10, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: posterior ventral tegmental area | 200 | Naive | In progress |
| P50 DA037844 Y5-10, Project 1: Neurogenetic Substrates of Cocaine Addiction | Paul Meyer, University at Buffalo | Brain: posterior ventral tegmental area | 145 | Exposure to cocaine | Tissue collected |
| P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: orbitofrontal cortex | 82 | Naive | Complete, the data is in RatGTEx |
| P50 DA037844 Y5-10, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: nucleus accumbens core | 200 | Naive | In progress |
| U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model | Suzanne Mitchell, Robert Hitzemann, Oregon Health & Science University | Brain: nucleus accumbens core | 193 | Behavior testing: Delay discounting | Complete, the data is in RatGTEx |
| P50 DA037844 Y5-10, Project 1: Neurogenetic Substrates of Cocaine Addiction | Paul Meyer, University at Buffalo | Brain: nucleus accumbens core | 147 | Exposure to cocaine | Tissue collected |
| P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: nucleus accumbens core | 77 | Naive | Complete, the data is in RatGTEx |
| U01 DA050239: Single-cell Resolution analysis of chromatin accessibility and gene expression changes in a model of drug addiction | Francesca Telese, UC San Diego | Brain: nucleus accumbens | 100 | Exposure to oxycodone | Collected |
| P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: lateral habenula | 82 | Naive | Complete, the data is in RatGTEx |
| U01DA044468; Genomic analysis of avoidance learning in addiction | Tom Jhou, University of Maryland | Brain: lateral habenula | 80 | Extreme high and low phenotypes in cocaine-avoidance and punishment resistance | In progress |
| P50 DA037844 Y5-10, Project 1: Neurogenetic Substrates of Cocaine Addiction | Paul Meyer, University at Buffalo | Brain: agranular insular cortex | 150 | Exposure to cocaine | Tissue collected |
| P50 DA037844 Y5-10, Project 1: Neurogenetic Substrates of Cocaine Addiction | Paul Meyer, University at Buffalo | Brain: prelimbic cortex | 141 | Exposure to cocaine | Tissue collected |
| P50 DA037844 Y5-10, Project 1: Neurogenetic Substrates of Cocaine Addiction | Paul Meyer, University at Buffalo | Brain: infralimbic cortex | 141 | Exposure to cocaine | Tissue collected |
| P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration | Hao Chen, University of Tennessee Health Science Center | Brain: infralimbic cortex | 83 | Naive | Complete, the data is in RatGTEx |
| R01DK120667: Systems genetics to identify neuronal genes for diet-induced obesity | Leah Solberg Woods, Wake Forest University | Brain: hypothalamus | 500 | High fat and Low fat diets, males and females | In progress |
| U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model | Suzanne Mitchell, Robert Hitzemann, Oregon Health & Science University | Brain: basolateral amygdala | 191 | Behavior testing: Delay discounting | Complete, the data is in RatGTEx |
| R01 EY021200: Genetic Modulators of Glaucoma | Monica Jablonski, University of Tennessee Health Science Center | Eye | 53 | Healthy HS rats | Complete, the data is in RatGTEx |
| R01DK106386: ystems genetics of adiposity traits in outbred rats | Leah Solberg Woods, Wake Forest University | Liver | 411 | All males, normal chow | Complete, the data is in RatGTEx |
| R01DK106386: ystems genetics of adiposity traits in outbred rats | Leah Solberg Woods, Wake Forest University | Adipose tissue | 411 | All males, normal chow | Complete, the data is in RatGTEx |