About Rat BodyMap

Project Design

The rat has been used extensively by the pharmaceutical industry and academic community as an animal model to test drug and chemical toxicities, evaluate the mechanisms of drug effects and understand human diseases. Although several large community-wide efforts are preparing a catalog of genes expressed during normal development of the mouse[1-2], such efforts are less advanced for the rat. Furthermore, the rat genome is still incomplete, containing many gaps and missing genes, and the rat transcriptome is far from well annotated. Understanding the transcriptome and alterations of mRNA expression during post-fetal development and between the sexes in the rat model will provide insights into disease susceptibility, drug efficacy and safety, and translation of pre-clinical findings to humans.

To study the rat transcriptome at single-base resolution, we constructed and sequenced 320 RNA-seq libraries from 320 individual RNA samples derived from 32 Fischer 344 rats. Ten organs were evaluated per sex (i.e., adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testis or uterus), and at four developmental stages (8 rats, 4 male and 4 female, per stage) (i.e., early immature, 2 weeks old; puberty, 6 weeks old; adult, 21 weeks old; and aged, 104 weeks old). To monitor the quality of the RNA-Seq, we added External RNA Control Consortium (ERCC) spike-in controls in an amount equivalent to 1% of the mRNA in each rat RNA sample before library construction. RNA-Seq libraries were constructed from individual biological samples and each library was sequenced 2–3 times. Using the Illumina HiSeq 2000 platform, we generated ~13.2 billion reads of 50 bp single-end RNA-Seq data with an average of 40 million sequence reads per sample.

Data Statistics

Libraries 320
Genes 40,064
Transcripts 65,167
Low-expressed genes 3,451
Always-expressed genes 15,894
Invariantly-expressed genes 776
Organ-enriched genes 3,413
Age-dependent genes 18,640
Sex-dependent genes 10,445


Rat BodyMap is a database that contains a set of rat RNA-Seq data which are initially generated. RNA-Seq data were generated and analyzed by SEQC Rat Body Map team.

1. Armit, C. et al. eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome. Mamm Genome 23, 514-524 (2012).
2. Henry, A.M. & Hohmann, J.G. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord. Mamm Genome 23, 539-549 (2012).