Strains

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RGD Strains

What is a strain?

Rats that are used in a laboratory come from different sources; most of these are derived from Rattus norvegicus. An inbred strain is one whose background can be defined and is named by the nomenclature conventions."

Normally the strains are named following the nomenclature guidelines. This is generally a unique, brief symbol made up of upper case, roman letters or a combination of letters and numbers beginning with a letter.

What types of Strains does RGD have information about?

RGD currently houses information about strains of the following types:

inbred
mutant
congenic
transgenic
recombinant_inbred
consomic
outbred
segregating_inbred
coisogenic
hybrid
advanced_intercross_line
conplastic

Click here for definitions of the rat strain types.

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RGD Definition
"Rats that are used in a laboratory come from different sources; most of these are derived from Rattus norvegicus. An inbred strain is one whose background can be defined and is named by the nomenclature conventions." Normally the strains are named following the nomenclature guidelines. This is generally a unique, brief symbol made up of upper case, roman letters or a combination of letters and numbers beginning with a letter. Rat Strain Registration: RGD tries to maintain a comprehensive list of all the rat strains available worldwide. This includes strain characteristics which are readily accessible by the rat community. To achieve these goals we are looking for community support in this effort in the following ways: If you maintain rat strains at your institution, please submit your rat strain data using our online registration form at RGD. During the process of registration we assign a unique RGD ID to your strain and ask you to please use this ID in your publications. If you are in the process of developing a new strain please inform RGD.Data@mcw.edu. We can assist in naming your strain and can reserve that symbol for you. We keep all this information non-public and release it only when your paper is published or you allow us to do so. Strain Submission: Please use our online strain registration form to submit your strain data to RGD. If you have multiple strains to submit please contact us at RGD.Data@mcw.edu and we can send you a strain template and guidelines to facilitate this process. If you do not have an ILAR code for your group please contact us and we can assist you in getting an ILAR code for your research group, institution or company. Strain Nomenclature: A click on 'Strain Nomenclature' goes to a page that has links to the guidelines that are approved by the Rat Genome Nomenclature Committee and the International Committee on Standardized Genetic Nomenclature for Mice. Here, one can find a quick guide to Rat Strain Nomenclature which is a condensed version (http://rgd.mcw.edu/nomen/quick_guide_strain_nomenclature.html ) of the main document. This lists the strain types, their characteristics, and a breif description what the root of the name should be. [ back to top ]
Finding Strain information
1. Using the Strain Search The Strain Search, reached by clicking the 'Strains' panel on the home page, is a quick route to finding strains. This will search Strain symbols and names only when a keyword is entered. The search will provide a list of matching strains with links to their report pages (see below). One can also use the General Keyword Search at the top right (See General RGD Search help for more information). [ back to top ] 2. Using the Classic Strain Search Form - Provides more customizable options, accessed by clicking 'Switch to classic strain search' on 'Strain Search' page. Quick Guide The users have a choice to search the strains by entering any of the keywords that describe a strain or they can even highlight the search fields already available to them and then click search strains to get all the information regarding a strain of interest Users also have a choice to view the list of strains available in RGD and highlight the strain of their interest to get a detailed report for this strain. TIP: to facilitate scrolling down highlight the column and enter the first letter of the strain of interest Note: Selecting a 'primary' strain such as BN (no substrain designation) will show the data for BN and all associated substrains of BN in RGD (BN/Cub-lx, BN/SsNHsd, etc). Selecting a strain with a specific substrain designation will show you the data for that strain alone. This is to facilitate comparison of strains and substrain information. Below is a more detailed explanation of each element of the search form, which will allow you greater flexibility to refine your searches. Strain Symbol/Alias/Keyword Enter a strain symbol, alias or keyword to search for. The asterisk '' is an accepted wildcard. Sample keyword searches include Hypertension, Diabetes, cancer, etc. The returned list of hits shows the keyword in the context of the text in the strain record to aid in identification of meaningful hits. Search Fields* Restrict the strain fields searched, multiple selections are allowed, the fields contain information on the following: Symbol - the strain symbol itself Origin - text describing the origin of the strain or colony. Anatomy - anatomical notes about the strain Behavior - observations on the behavior of the strain Drugs and Chemicals - interactions and responsiveness to various drugs and chemicals Immunology - Immunological notes about the strain Infection - Susceptibility and response to infection Lifespan and Spontaneous Disease - Typical lifespan of this strain, known disease-susceptibilities Physiology and Biochemistry - results pertaining to the physiology or biochemistry of this strain Reproduction - notes on the reproductive success of this strain, litter sizes, etc. [ back to top ]
The RGD Strain Report Pages
RGD strives to collect facts related to all rat strains worldwide. The strains are submitted by individual researchers, rat providers, and incorporated from QTL and strain publications that are curated by RGD curators. Below is a description of each of the information sections available on a strain report page. All the different types of strains are named according to the strain nomenclature guidelines approved by the Rat Genome Nomenclature Committee and the International Committee on Standardized Genetic Nomenclature for Mice. The strain symbol is generally a brief symbol comprising of upper case, lower case letters and sometimes roman numerals followed by the ILAR code for that particular group. Researchers can get a 3-4 letter ILAR code for their group by contacting RGD at RGD.Data@mcw.edu. To facilitate maneuvering in the strain report page, the page is divided into sections. Not every field will be in every report: General Section More on this Strain Section Annotation Section Region Section Additional Information Section General The 'General' tab contains most of the basic information about the strain.

Symbol: This is the official symbol assigned to this strain according to the strain nomenclature guidelines. This is a combination of strain and substrain designations for inbred strains (or symbol and ILAR code for other strain types).

Strain: The official strain symbol.

Substrain: The official substrain symbol - this can be a collection of ILAR lab codes defining the history of this particular strain. Can also be found in pulldown section below with links to the strain report pages.

Full Name: If the strain has a text name then it is displayed here; this is not visible if no name is associated to the strain, as in this example.

Ontology ID: The identification number of the strain ontology term assigned by RGD, linked to the term in the ontology browser. In the strain ontology, rat strains are organized in a hierarchical fashion based on the type of strain and the way they were developed.

Also known as: Old symbols and synonyms that were used for the strain. If a strain is renamed to comply to the guidelines of strain nomenclature, then the symbol used by researchers is mentioned here.

Type: One word description of the category of the strain - inbred, congenic, consomic, outbred.

Source: The name of the lab, department, university or company from where this particular strain can be obtained.

Origin: A brief description of the mothod used to generate this strain.

See Also: Links to other substrains of this strain, or the main strain for this substrain. These pages often have extra information about a particular strain, especially the parental strain page (e.g. BN would be the parental strain for the BN/Ssn substrain). Not present in this example.

Genetic Markers: Genotype for standard genetic markers used in the characterization of inbred strains.Not present in this example.

Coat Color: The coat color of this strain - e.g. Albino, brown, white.

Inbred Generations: The number of generations that this strain has been inbred at the time the data was curated.

Model: If the strain is a model fo rany specific disease as mentioned by the authors of a paper then this informations is displayed here. Not present in this example.

More on this Strain

This section at the top right side of the page has more information about strains.

Strain Nomenclature

Strain Registration

RGD Object Information

The RGD ID for the strain, the date the record was created in the database, the species, the date the strain information was last updated, and the status of the record in the database appear in this box.

Pulldown Menus

Substrains

Annotation

This section has subsections containing ontology annotations assigned to the strain. These are organised by ontology type, which includes the Mammalian Phenotype ontology and disease vocabulary. Additional subsections contain information about phenotype analysis in the PhenoMiner tool, annotations to the strain in disease portals and a list of curated references for the strain. By default the subsections are closed to facilitate navigation through the page but each can be expanded with a single click anywhere on the title bar.

Disease Annotations

These annotations represent disease to strain associations manually curated from the biomedical literature. The terms come from a disease vocabulary which merged OMIM and MeSH disease vocabularies. The combined vocabulary was created at the Comparative Genomics Database (CTD), disease annotations are followed by the evidence codes IAGP or IED and the reference from where this annotation was derived.

Phenotype Annotations

These annotations represent the association of strains with particular mammalian phenotypes. The terms come from the Mammalian Phenotype Ontology developed at MGI (http://www.informatics.jax.org/, Genome Biol. 6(1):R7. Epub 2004 Dec 15.) The terms are supported by the same group of evidence codes as used for disease vocabulary annotations.

Phenotype Values via Phenominer

This is a list of all the Phenotypes that are measured using this strain. These are retrieved from the RGD PhenoMiner tool, which houses phenotype data. A click on 'View chart' goes to the PhenoMiner tool displaying the details of the phenotypes. 'Download data table' opens a downloadable version of this data as an Excel spreadsheet and 'View expanded data table' gives an enhanced version of this data.

RGD Disease Portals

Strain report pages are linked to disease portals in which this strain is annotated. If a strain is a model for a particular disease then it is mentioned in the portal's 'Rat Strain Models' tab.

References - curated

A list of all references that have been used by the RGD curation team for annotating this strain. These link out to the RGD Reference report pages which have the abstracts of the articles. There is a link to PubMed from this page.

Region

Strain QTL Data

This is a list of QTLs that have been identified using this strain, and are annotated to it. The QTLs are linked to the RGD QTL report pages.

Position Markers

This section is visible only in the congenic strains that have SSLPs/genes/ESTs used as markers to define the introgressed segment.

Additional Information

RGD Curation Notes (Strain Characteristics)

These are free text notes that give us the information that is not captured by the disease and phenotype annotations, These are curated under the following headings:
Anatomy, Behavior, Characteristics, Drugs and Chemicals, Infection, Immunology, Life Disease, Physiology and Biochemistry, Reproduction and other.

Nomenclature History

This indicates when the strain was named and lists dates of any symbol changes.

Strain Curation Process in RGD

RGD curates all the strains (inbred, congenic, consomics, etc.) that are mentioned in all rat QTL papers. Besides this the strains submitted to RGD from researchers and vendors are curated. RGD has weekly searches set up in PubMed based on the different strain types and names of authors who work on specific strains. These searches bring lists of papers which are curated by RGD.

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