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. 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. Scientists compare rat genome with human, mouse analysis yields new insights into medical model, evolutionary process. 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.
The draft sequence of the rat genome is published this month rat genome sequencing project consortium, nature 1 april 2004 doi. Was much debate about the overall value of the rat genome sequence. Currently, rgd combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. The site also hosts data mining and analysis tools for rat genomics and physiology. Pdf the rat genome database 20data, tools and users. Exploring phenotypic data at the rat genome database n. For quick access to the most recent assembly of each genome, see the current genomes directory. 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 rgd has grown considerably in terms of number of data objects, annotations using ontologies and tools for data integration. Gene reports include a comprehensive description of function and biological process as well as disease, expression, regulation and phenotype information. Rat genome reveals supercharged evolution new scientist. The rat genome database rgd, provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the.
The rat genome database rgd has been the premier resource for. 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 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. There are known physiologic differences between the numerous outbred stocks and inbred strains of rats.
A comparative genomics platform human genomics full text. Who, what, where, why article pdf available in plos computational biology 511. The rat genome database is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Mar 31, 2004 rat genome reveals supercharged evolution. 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. Based on its manualcuration initiatives, rgd has generated disease portals, which provide easy access to multiple genomic and genetic data types associated. Scientists compare rat genome with human, mouse nhgri. What everybody should know about the rat genome and its. How many gene transcripts are there in rat genome latest. 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 extra sequence data now available provide an opportunity to upgrade the rat assembly, and work is underway to incorporate these new data into a.
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. The rat genome database 20data, tools and users pdf. The rat genome database 20data, tools and users ncbi nih. This page contains links to sequence and annotation data downloads for the genome assemblies featured in the ucsc genome browser. The ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. 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. 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 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. A comparative genomics platform human genomics full. The rat genome database rgd has been the premier re source for rat genetic, genomic and phenotypic data since its creation in 1999. 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 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 has been the premier resource for rat genetic, genomic and phenotypic data since its creation in 1999. Information on inbred, outbred, mutant, congenic, consomic and other types of rat strains is also provided. The rat genome database rgd was started 10 years ago to. 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.
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. Rat genome sequence reignites preclinical model debate. Currently, rgd combines genetic, genomic, pathway, phenotype and strain information. Dwinell2 abstract rattus norvegicus, the laboratory rat, has been a crucial model for. A wide variety of traits associated with multiple physiological systems are represented by the qtls at rat genome database rgd. The laboratory rat, rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have direct relevance to.
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. 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. 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 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. The rat genome database api allows developers to programmatically access information and annotations stored in the rat genome database rgd. Whole exome sequencing in the rat bmc genomics full text. Pdf tools and strategies for physiological genomics. Using an insilico approach, we designed probes targeting the rat.
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. Jan 01, 2005 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. 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 similar species rattus norvegicus, the brown rat or wharf rat, has also been carried worldwide by ships in recent centuries. The rgd hosts rat genomics, genetics, physiology, and functional data. Rat genome database an overview sciencedirect topics. It also includes data on comparative genomics between rats, humans, and mice. 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. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The rat genome database houses genomic, genetic, functional, physiological, pathway and disease data for the laboratory rat as well as comparative data for. Exploring genetic, genomic, and phenotypic data at the rat.
Together with recent developments in cloning technologies, this heralds an important phase in rat research. The rat genome database rgd, is an nihfunded project whose stated mission is to collect, consolidate and integrate data generated. Exploring human disease using the rat genome database. Rat genome and model resources mary shimoyama, jennifer r. Roughly 200 years after being tamed, bred and adopted as sciences favourite laboratory animal, the brown norway rat has. The rat genome database rgd was started 10 years ago to provide a core genomic resource for rat researchers. Exploring human disease using the rat genome database mary shimoyama1, stanley j.
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. 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 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 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. 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. Howard jacob presented the latest developments for the rat genome database. 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. Formed in late 1999, the rat genome database rgd, will be 20 in 2020, the year of the rat. I have found the rat genome database to be very good but have only been working on genomics so far, not rnaseq.
Because the laboratory rat, rattus norvegicus, has been used as a model for complex. The rat genome database rgd, is an nihfunded project whose stated mission is to collect, consolidate and integrate data generated from ongoing. 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 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 is an important animal model for pharmacology, toxicology, physiology and pathology.
Insights from the rat genome sequence genome biology full. 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. 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. The rat provides a wide variety of experimental approaches. The rat genome database rgd serves as the primary rat data repository, providing both manual and computationally collected data from other databases. Because of the rat s utility in diverse studies and its use in studying human disease, rgd has continued to attract. Because of the rats utility in diverse studies and its use in studying human disease, rgd has continued to attract. Call for papers updates on mapping quantitative trait loci rat genome database. 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. It also includes data on comparative genomics between rats. Rat genome databases, repositories, and tools springerlink. Thomas hayman1, shurjen wang1, omid ghiasvand1, jyothi thota1 and melinda r.
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