Rat dataset: a animal model of human disease

For over 200 years, the common laboratory rat has been used as a model of human disease, including evaluating chemical toxicities and understanding drug mechanisms.

Rat dataset: a animal model of human disease

An earlier international study, a paper published in Nature, has completed a high-quality, draft sequence of the genome of the laboratory rat, and has used that data to explore how the rat's genetic blueprint stacks up against those of mice and humans.

the Rat Genome Sequencing Project Consortium describes its efforts to produce and analyze a draft sequence of the Brown Norway strain of the laboratory rat (Rattus norvegicus)

In their Nature paper, the rat genome(2.75 billion base pairs) is smaller than the human genome(2.9 billion base pairs), the rat genome contains about the same number of genes as the human and mouse genomes. Furthermore, almost all human genes known to be associated with diseases have counterparts in the rat genome and appear highly conserved through mammalian evolution, confirming that the rat is an excellent model for many areas of medical research.

The rat is used extensively by the pharmaceutical, regulatory and academic communities to test drug and chemical toxicities, to evaluate the mechanisms underlying drug effects and to model human diseases. Areas in which rat models have already helped to advance medical research include: cardiovascular diseases (hypertension); psychiatric disorders (studies of behavioral intervention and addiction); neural regeneration; diabetes; surgery; transplantation; autoimmune disorders (rheumatoid arthritis); cancer; wound and bone healing; and space motion sickness. In drug development, the rat is routinely employed to demonstrate therapeutic efficacy and assess toxicity of drug compounds prior to human clinical trials. The genome sequence will facilitate all of these studies, as well as help researchers better pinpoint the crucial areas of biological difference between rats and humans.

Although several community-wide efforts are preparing a catalogue of genes expressed during normal development of mice1,2 and humans3,4, 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 not well annotated. Next-generation sequencing technologies have revolutionized genomic research and allow the genome and transcriptome of any organism to be explored without a priori assumptions and with unprecedented throughput.

We create a web-based, open-access Rat dataset of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model.

Overview of the Rat dataset in CNGBdb

The Rat dataset contains a series of research about rat model, such as A catalog of the Sprague-Dawley (SD) rat gut metagenome, Cranial irradiation in juvenile female rats induces late-onset obesity and metabolic disturbances, Sigmodon hispidus Genome sequencing and assembly, Rattus norvegicus Transcriptome or Gene expression, etc.

In summary, we have generated a comprehensive rat dataset encompassing genome sequencing and assembly, transcriptome, or gene expression, data volume 2.11Tb. As a unique public resource for rat genome projects, this dataset is expected to provide a comprehensive platform for biomedical research by enabling increased understanding of human diseases and improved assessment of drug efficacy and toxicity with the rat model.

Please keep on paying attention to CNGBdb.

1.Yu, Y. et al. A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat. Commun. 5:3230 doi: 10.1038/ncomms4230(2014).
2.Scientists Compare Rat Genome With Human, Mouse, https://www.genome.gov/11511308/2004-release-scientists-compare-rat-genome