The rat genome database rgd curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease. This page contains links to sequence and annotation data downloads for the genome assemblies featured in the ucsc genome browser. I have found the rat genome database to be very good but have only been working on genomics so far, not rnaseq. Jan 01, 2005 the rgd has grown considerably in terms of number of data objects, annotations using ontologies and tools for data integration. Thus a centralized rat genome database is needed to enable investigators.
Resources for rat researchers are extensive, including strain repositories and databases all around the world. Hl990 is the establishment of a rat genome database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. The extra sequence data now available provide an opportunity to upgrade the rat assembly, and work is underway to incorporate these new data into a genome upgrade planned. Information on inbred, outbred, mutant, congenic, consomic and other types of rat strains is also provided. Rat genome database an overview sciencedirect topics. The national human genome research institute nhgri and the national heart, lung and blood institute nhlbi have supported a rat genome sequencing project to produce 7x draft coverage of the rat genome in a mixture of whole genome shotgun and bacterial artificial chromosome bacbased sequence. Based on its manualcuration initiatives, rgd has generated disease portals, which provide easy access to multiple genomic and genetic data types associated. A comparative genomics platform human genomics full.
Rat genome and model resources mary shimoyama, jennifer r. The rat genome database houses genomic, genetic, functional, physiological, pathway and disease data for the laboratory rat as well as comparative data for. On june 22, 2000, ucsc and the other members of the international human genome project consortium completed the first working draft of the human genome assembly, forever ensuring free public access to the genome and the information it contains. Genetics and molecular biology genome science of the rat takashi kuramoto and toshikazu ushijima encyclopedia of life support systems eolss genome science of the rat takashi kuramoto and toshikazu ushijima national cancer center research institute, tokyo, japan keywords. The rat genome database 20data, tools and users pdf. Formed in late 1999, the rat genome database rgd, will be 20 in 2020, the year of the rat. Exploring phenotypic data at the rat genome database n. Who, what, where, why article pdf available in plos computational biology 511. The rat genome database rgd, provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the. The extra sequence data now available provide an opportunity to upgrade the rat assembly, and work is underway to incorporate these new data into a. Exploring genetic, genomic, and phenotypic data at the rat. The advances in generating and utilizing new genomic tools for the rat has produced an increased demand for central accessibility of rat data to enhance access to the data and improve its correlation with the existing physiological and phenotypic information about the rat. Together with recent developments in cloning technologies, this heralds an important phase in rat research.
The national human genome research institute nhgri and the national heart, lung and blood institute nhlbi have supported a rat genome sequencing project to produce 7x draft coverage of the rat genome in a mixture of whole genome shotgun and. Smith, elizabeth bryda, takashi kuramoto, laura saba, and melinda dwinell mary shimoyama, phd, is an associate professor in the department of biomedical engineering at marquette university and the medical college of wisconsin in milwaukee, wisconsin. The site also hosts data mining and analysis tools for rat genomics and physiology. The rat genome database rgd is the model organism database tasked with the curation and integration of genomic data with a focus on the use of the rat as a model system for the study of the genetic basis of complex phenotypes. Hl990, was the establishment of a rat genome database to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. The rat provides a wide variety of experimental approaches. Whole exome sequencing in the rat bmc genomics full text. The rat genome database houses genomic, genetic, functional, physiological, pathway and disease data for the laboratory rat as well as comparative data for mouse and human. The laboratory rat, rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have direct relevance to. Apr 30, 2004 the availability of the rat genome sequence, and detailed threeway comparison of the rat, mouse and human genomes, is revealing a great deal about mammalian genome evolution. Currently, rgd combines genetic, genomic, pathway, phenotype and strain information. The rat genome database rgd is the model organism database tasked with the curation and integration of genomic data with a focus on the use of the rat as a model system for the study of the genetic basis of complex phenotypes 6. Rat genome reveals supercharged evolution new scientist.
A wide variety of traits associated with multiple physiological systems are represented by the qtls at rat genome database rgd. Using an insilico approach, we designed probes targeting the rat. There are known physiologic differences between the numerous outbred stocks and inbred strains of rats. Howard jacob presented the latest developments for the rat genome database. Since 1850, rattus norvegicus the laboratory rat has been the model organism of choice for many investigations into the physiological mechanisms of complex diseases and the genetic and environmental factors that affect disease onset, progression and severity lindsey, 1979. The rat genome database rgd has been the premier re source for rat genetic, genomic and phenotypic data since its creation in 1999. The rat genome database rgd, is an nihfunded project whose stated mission is to collect, consolidate and integrate data generated from ongoing. Exploring human disease using the rat genome database mary shimoyama1, stanley j. Genetic models phenominer quantitative phenotypes expected ranges quantitative phenotype phenominer term comparison hybrid rat diversity panel phenotypes gerrc gene editing rat resource center phenotypes in other animal models animal husbandry strain medical records phylogenetics strain availability calendar rats 101 submissions photo archive. The availability of the rat genome sequence, and detailed threeway comparison of the rat, mouse and human genomes, is revealing a great deal about mammalian genome evolution. Jun 20, 2018 the rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. The rat genome database rgd has been the premier resource for. For quick access to the most recent assembly of each genome, see the current genomes directory.
How many gene transcripts are there in rat genome latest. Jul 15, 2006 the laboratory rat, rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have direct relevance to human. The rat genome database rgd serves as the primary rat data repository, providing both manual and computationally collected data from other databases. Mar 31, 2004 rat genome reveals supercharged evolution. The results show a summary of the number of rat, human and mouse genes annotated to the selected terms, the list of individual genes by species, the gviewer for the rat genes with the option of viewing the human or mouse gviewer, or the rathuman or ratmouse synteny, and an overview of go annotations by vocabulary type. The rat genome database is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Call for papers updates on mapping quantitative trait loci rat genome database. Insights from the rat genome sequence genome biology full. Oct 17, 2005 the rat genome database rgd is the model organism database tasked with the curation and integration of genomic data with a focus on the use of the rat as a model system for the study of the genetic basis of complex phenotypes. Rat genome database pdf 75 gigabases, gb is smaller than the human. The rat genome database 20data, tools and users ncbi nih. The draft sequence of the rat genome is published this month rat genome sequencing project consortium, nature 1 april 2004 doi. The rat genome database rgd has been the premier resource for rat genetic, genomic and phenotypic data since its creation in 1999.
The rgd has grown considerably in terms of number of data objects, annotations using ontologies and tools for data integration. Table downloads are also available via the genome browser ftp server. It also includes data on comparative genomics between rats, humans, and mice. Dwinell2 abstract rattus norvegicus, the laboratory rat, has been a crucial model for. Select a species human bushbaby chimpanzee gibbon gorilla human macaque marmoset mouse lemur orangutan tarsier guinea pig kangaroo rat mouse pika rabbit rat squirrel tree shrew alpaca cat cow. Thomas hayman1, shurjen wang1, omid ghiasvand1, jyothi thota1 and melinda r. Pdf tools and strategies for physiological genomics. The laboratory rat, rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and. The rgd hosts rat genomics, genetics, physiology, and functional data.
Because of the rat s utility in diverse studies and its use in studying human disease, rgd has continued to attract. Exploring human disease using the rat genome database. What everybody should know about the rat genome and its. To see the differences between different rat annotations i would strongly recommend mapping them to the genome with gmap, and or importing them into a genome browser for visual comparison at multiple loci. The ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. Currently, rgd combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. Rat genome sequence reignites preclinical model debate. The wealth of data at rgd includes genes and qtls for rat, human and mouse, as well as polymorphic markers for rat and human table 1. The rat genome database rgd was started 10 years ago to provide a core genomic resource for rat researchers. Scientists compare rat genome with human, mouse nhgri. The concentration of qtls in a few significant areas reflects the value of the rat as a model for diseases related to those traits and the experiments conducted by rat researchers to date. Here, we report development and testing of a probe set for whole exome sequencing wes to detect sequence variants in exons and utrs of the rat genome. The rat genome database rgd, is an nihfunded project whose stated mission is to collect, consolidate and integrate data generated. We initiated efforts to increase biological content in the database and to attach it to the genome, while maintaining our core strengths as a comprehensive database of rat genomic data and genomic tools.
The rat genome database rgd is an extensive, free resource filled with information regarding the different phenotypes, models, and genomic tools used in rat research laulederkind et al. The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. The rat genome database is the model organism database for the rat and is hosted by the medical college of wisconsin. The rat genome database rgd was started 10 years ago to. Pdf the rat genome database 20data, tools and users. Scientists compare rat genome with human, mouse analysis yields new insights into medical model, evolutionary process. Was much debate about the overall value of the rat genome sequence. Jan 28, 2015 the rat genome database rgd has been the premier resource for rat genetic, genomic and phenotypic data since its creation in 1999. Because the laboratory rat, rattus norvegicus, has been used as a model for complex. The rat is an important animal model for pharmacology, toxicology, physiology and pathology. A comparative genomics platform human genomics full text.
Gene reports include a comprehensive description of function and biological process as well as disease, expression, regulation and phenotype information. The similar species rattus norvegicus, the brown rat or wharf rat, has also been carried worldwide by ships in recent centuries. Roughly 200 years after being tamed, bred and adopted as sciences favourite laboratory animal, the brown norway rat has. Rat genome databases, repositories, and tools springerlink. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The laboratory rat, rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. Because of the rats utility in diverse studies and its use in studying human disease, rgd has continued to attract. The rat has been the subject of scientific research for over 150 years and in that time it has developed as a highly popular organism for physiological, pharmacological and genetic research in a wide variety of areas fundamental to human health.
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