About RatGTEx

Associated Studies

The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats (Preprint)

Other publications will be posted when available.

More info on the ratgenes.org eQTL page.

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.

TissueAbbreviationSamplesOriginating study
Infralimbic cortexIL81P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
Lateral habenulaLHb81P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
Nucleus accumbens coreNAcc75P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
Orbitofrontal cortexOFC80P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
Prelimbic cortexPL80P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration
EyeEye51R01 EY021200: Genetic Modulators of Glaucoma
Basolateral amygdalaBLA185U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model
Nucleus accumbens coreNAcc2188U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model
Prelimbic cortexPL2191U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model
AdiposeAdipose411R01DK106386: Systems genetics of adiposity traits in outbred rats
LiverLiver401R01DK106386: Systems genetics of adiposity traits in outbred rats

Contact

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

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.

Data Specifications

The datasets provided in this portal conform to the following specifications to facilitate comparisons across tissues.

Processing

The ratgtex-pipeline repository contains all RNA-Seq and eQTL mapping pipeline code. The ratgtex-server-data repository contains code that processes those results into additional data files for download and for the API.

Formats

Gene expression ({tissue}.expr.{units}.bed.gz)

Expression tables are provided in BED format, with four columns describing the gene plus one column per sample. Only the transcription start sites are specified, not the whole gene length.

All significant cis-eQTL gene-SNP pairs ({tissue}.cis_qtl_signif.txt.gz)

A compressed tab-separated table.

Strong associations from trans-eQTL mapping ({tissue}.trans_qtl_pairs.txt.gz)

All measured SNPs genome-wide were tested against expression of each gene, and pairs with p-value < 1e-5 and > 5 Mb TSS distance are included here. Rows are sorted by variant location.

Conditionally independent cis-eQTLs (eqtls_indep.txt)

A table of cis-eQTLs from all tissues. Stepwise regression was used to test for cis-eQTLs beyond and uncorrelated with the top cis-eQTL per gene.

Top association per gene (top_assoc.txt)

A table of the strongest variant-gene association per gene per tissue, even if not significant.