Rat transcriptomics datasets

The expression of ∼7000 rat genes was measured by array across 11 peripheral and 15 brain tissues in Sprague Dawley, Wistar and Wistar Kyoto rats, using two to three samples from different or same strain per each tissue (36). Normalized data were obtained via BioGPS. The annotation file for the RG_U34A array chip used in the study was used for mapping the 7999 probeset identifiers to a total number of only 4731 STRING identifiers. 25 of the 26 tissue names could be mapped to BTO terms.

The Rat transcriptomic BodyMap study used RNA-seq to profile expression across 11 tissues and four developmental stages for 32 individuals in Fisher 344 rats (37). We obtained processed data for the adult developmental stage with expression measured in FPKM units and annotated with Ensembl gene identifiers from ArrayExpress (E-GEOD-53960). We further mapped these to 19 554 STRING identifiers using the dictionary and averaged the expression values across biological replicates.

This data come from the same study as the previously described MIT RNA-seq mouse atlas (31). Expression was measured using RNA-seq on polyA-selected RNA from the same nine tissues with three biological replicates. We downloaded the FASTQ files from ArrayExpress (E-MTAB-2800) and processed them using our pipeline, thereby quantifying expression for 19 566 STRING identifiers.