About RatGTEx

Associated Studies

Manuscripts in preparation.

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

• Genome assembly: Rnor_6.0 (GCA_000001895.4)
• Annotations: Ensembl Rat
• RNA-Seq read counts, transformed as log₂(count+1), were used to compute cis-eQTL effect sizes (allelic fold change).
• Inverse-quantile normalized expression values were used for eQTL mapping.
• eQTL mapping: tensorQTL. cis-eQTL mapping tested cis-windows +/- 1 Mb from each gene's transcription start site.

Formats

Gene expression

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.

• #chr Chromosome name, e.g. '1'
• start Transcription start site. Coordinates in BED format are 0-based, so this is one less than the position as it is typically represented.
• end One higher than the start value. Thus, this would be the typical coordinate to represent the TSS.
• gene_id Ensembl gene ID
• {sample} Each additional column is labeled with the sample or rat ID and contains log2(count+1), TPM, or inverse-quantile normalized values.

All significant cis-eQTL gene-SNP pairs (*.cis_qtl_signif.txt.gz)

A compressed tab-separated table.

• gene_id Ensembl gene ID
• variant_id SNP ID (e.g. chr1:669562)
• tss_distance SNP position - TSS position, oriented on the gene's strand
• af Alternative allele frequency
• ma_samples Number of samples with minor allele
• ma_count Total number of minor alleles (i.e. no. het. + 2 * no. hom. alt.)
• pval_nominal Nominal p-value
• slope Coefficient for the SNP genotype in the linear model
• slope_se Standard error of the slope
• pval_nominal_threhsold Gene-tissue-specific nominal p-value significance threshold as determined by permutations and transcriptome-wide FDR

Strong associations from trans-eQTL mapping (*.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.

• variant_id SNP ID (e.g. chr1:669562)
• gene_id Ensembl gene ID
• pval Nominal p-value
• slope Coefficient (slope) for the SNP genotype in the linear model
• slope_se Standard error of the slope
• af Alternative allele frequency