Finding an Resource Identification Initiative(RII) ID for a mouse strain
RII: http://scicrunch.com/resourcesMouse Genome Informatics (MGI): http://www.informatics.jax.org/
Background• Many researchers work at the level of the gene, but to accurately identify your
research organism requires identification at the level of genotype, which is the complete description of the allele composition (specific allele(s), zygosity) and the strain background. – Different alleles are important because of
• Different generation methods (targeted, transgenic, ENU induced, spontaneous, etc)• Different attributes (null/knockout, conditional-ready, modified isoform, inducible, etc)• Underlying biologically-relevant differences in construction (specific domain modification,
whole gene, etc)• Differences relevant to researcher protocols (how to genotype, etc)
– Different strain backgrounds are important because of• Modifier effects from the background• Altered phenotypic expression (ex. 5 tumors vs. 50 tumors, age of onset, etc)• Appropriate choice of control animals
• Disclaimer: MGI is working with RII to improve the content and clarity of information available on their site. This doc describes how to navigate right now, there are still bugs and “missing” info/capabilities
Starting from RII:1. Begin here. Search for organism.You can also begin by typing your gene into the search bar in the upper right, then filtering for organism
2. Notice tabs are now highlighted with “ORGANISMS” selected as default. Click on ANTIBODIES or TOOLS to change if desired.
3. Begin typing your gene name and select from the dropdown list (here, Pax2)
4. Expand sidebar filters by clicking on [+] symbols. All available options/filters are displayed
5. Narrow by selecting database and/or species. For mice, use MGI or IMSR (International Mouse Strain Resource) from “Database”. This walk through will use MGI, apply the filter by clicking “MGI”. The grey number indicates how many records there are in each, for MGI, each unique genotype is a record.
ZFIN = zebrafish; CGC = Caenorhabditis Genetics Center
6. If complex genotypes have been reported (i.e. Pax2 mutant and another gene mutation within the same animal) these will appear with multiple genes in “Affected Gene”. Click “Pax2” to filter for single marker genotypes
7. Select the specific mutant allele from “Genomic Alteration”. If you are not sure which allele, go to MGI and search “Pax2” or “Pax2tm1Pgr” for more details.
Attributes, links and more will (hopefully) be added soon to make this step easier.
Allele IDs use standardized nomenclature with “tm” = targeted mutation and last 3~5 digits being the lab code for the researcher or project that generated the mice. See http://www.informatics.jax.org/mgihome/nomen/allmut_quickhelp.shtml
Note that filters applied now appear on top. Click the X to remove
Finding your allele in MGI: Option 1. From a reference using MGI Reference Query
Finding your allele in MGI: Option 2. Using a gene search
Pax2
See next page…
Finding your allele in MGI: Option2. Using a gene search
Use “Category” column, and others to find alleles matching the description of your allele. Click allele hyperlinks to go to allele detail page.
See next page…
Confirm mutation description, locate original reference describing mutation generation
Carrying this Mutation: Mouse Strains: 1 strain availableThis strain is commercially available through one of the repositories indexed by the IMSR, so you may have purchased it.
See other references using this specific allele
8. Select specific allele
Resuming in RII:
9. Select strain background
10. Identify RII record that corresponds to your mouse
Describes zygosity: homozygous mutant
Describes strain genetic background
Goes to MGI genoview page
Compare RII with MGI
(from MGI’s Allele Detail page for Pax2tm1Pgr)
Homozygous for Pax2tm1Pgr/Pax2tm1Pgr
Genetic background: involves 129S1/Sv*129X1/SvJ*C57BL/6
See three genotypes homozygous for Pax2tm1Pgr/Pax2tm1Pgr
Row hm2 describes the genotype consistent with:Pax2tm1Pgr/Pax2tm1Pgr on a background that involves 129S1/Sv*129X1/SvJ*C57BL/6
Column hm2 describes phenotypes annotated to this specific genotype
Compare RII with MGI
(from MGI’s Allele Detail page for Pax2tm1Pgr)
Click catalog # in RII or row/column labels in MGI to go to the genoview popup
Find unique genotype ID in the url
Obtain RII ID
This is the RII ID code to include in your manuscript.
If a genotype does not already exist that matches your mouse, please contact MGI athttp://www.informatics.jax.org/mgihome/submissions/amsp_submission.cgi so we can create a (confidential) genotype prior to submission.