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.