• • Assembled by Dr. Joyce Repa, UTSW Medical Center

Gene-trap ES cell line resources:
International Gene-trap Consortium: http://www.genetrap.org/    
German Gene Trap Consortium (Germany)  13031        http://www.genetrap.de/
Sanger Inst. Gene Trap Resource (Cambridge, UK) 7354    http://www.sanger.ac.uk/PostGenomics/genetrap/
Soriano Lab Gene Trap Database (FHCRC, Seattle, USA)1627    http://www.fhcrc.org/science/labs/soriano/trap.html

Mouse suppliers:>
Federation of International Mouse Resources    http://www.fimre.org/
Mutant Mouse Regional Resource Centers http://www.mmrrc.org/about/generalInfo.html

Mouse resources:
Edinburgh Mouse Atlas (emap) and gene expression database (emage)   http://genex.hgu.mrc.ac.uk
European Mouse Mutant Archive (EMMA)—transgenic mouse repository http://www.emma.rm.cnr.it
Festing’s Inbred Strain Characteristics    http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
Insitut Clinique de la Souris (ICS)    http://www-mci.u-strasbg.fr/
International Mouse Strain Resource—aims to list all publicly available mouse strainsa   http://www.informatics.jax.org/imsr/index.jsp
Mouse Genome Informatics—access to data on the genetics, genomics, and biology of the mouse    http://www.informatics.jax.org
Mouse Knockout and Mutation Database—searchable database    http://www.biomednet.com/db/mkmd
Mymouse.org—aims to facilitate international collaborative research among mouse users    http://www.mymouse.org
Online Mendelian Inheritance in Man (OMIM)—catalogs relevant mouse models of human disease    http://www.ncbi.nlm.nih.gov
TBASE—database for transgenic and knockout mice    http://tbase.jax.org/
The GeneNetwork—bioinformatic resources for systems genetics and complex trait analysis   http://www.genenetwork.org/
Whole Mouse Catalog—information website    http://www.rodentia.com/wmc

Phenotyping:
Jackson Lab’s Mouse Phenome Database: http://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home
Mouse Metabolic Phenotyping Centers (NIDDK): http://www.mmpc.org/index.htm
EMPRESS (European consortium)
Examples of metabolic phenotyping tests and their standard operating procedures (SOPs)

Phenotype test                                                SOP website link
Energy expenditure    Body weight, food, and water intake                  http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_005_0.pdf
Body composition                                           http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_002_0.pdf
Cold test                                                        http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_001_0.pdf

Serum parameters      Cholesterol
Triglycerides                                                    http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/3_002_0.pdf
Free fatty acids                                                http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/3_003_0.pdf
Lipoproteins                                                     http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/3_004_0.pdf
Apolipoproteins                                                http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/3_A01_0.pdf
Bile Acids

Glucose tolerance      Intraperitoneal glucose tolerance test               http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_004_0.pdf
Meal tolerance test                                        http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_007_0.pdf
Oral glucose tolerance test                             http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/4_008_0.pdf

Ex vivo                    General histology techniques                            http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/15_001_0.pdf
H&E staining                                                 http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/15_016_0.pdf
Oil Red O staining                                          http://www.empress.har.mrc.ac.uk/EMPReSS/pdf/15_026_0.pdf

These protocols can be found on the EMPReSS website (http://www.empress.har.mrc.ac.uk/EMPReSS/servlet/EMPReSS.Frameset) (Green et al.,  Bioinformatics 21: 2930-1, 2005).

Metabolic Pathways:
Kyoto Encyclopedia of Genes and Genomes: http://www.genome.jp/kegg/pathway.html
Pathguide: the pathway resource list: http://www.pathguide.org/ (219 biological pathway resources)
Ingenuity: http://www.ingenuity.com
GenMAPP:  http://www.genmapp.org

Expression profiling:
Tissue distribution of most genes (Genomics Inst. Of the Novartis Res. Fnd): http://symatlas.gnf.org/SymAtlas/
Institute for Genomic Research http://pga.tigr.org
Gene Expression Omnibus  http://www.ncbi.nlm.nih.gov/geo
Jackson Laboratory http://www.informatics.jax.org/menus/expression_menu.shtml
Brain Atlas  http://brainatlas.org
Real-time PCR probe and primer database: http://medgen.UGent.be/rtprimerdb/
Quantitative PCR primer database;    http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer

Miscellaneous:
January issue of Nuclear Acids Research is the “Database Issue” each year.

Nuclear Receptor binding site identification:
http://www.nubiscan.unibas.ch.    Ref: Podvinec et al. NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Molecular Endocrinology 16: 1269-1279, 2002.
http://mordor.cgb.ki.se/NHR-scan   Ref: Sandelin, et al. Prediction of Nuclear Hormone Receptor Response Elements.  Molecular Endocrinology 19:595-606, 2005.

Quantitative real-time PCR resources (primer databases):
https://orf.invitrogen.com/lux/  Website for primer design algorithms.
http://pga.mgh.harvard.edu/primerbank/ Website listing qPCR primers for human and mouse genes.  Ref: Spandido, et al. Nucleic Acids Research 38:D792-D799, 2010.
http://web.ncifcrf.gov/rtp/gel/primerdb/   “QPDD” primer set (human and mouse/SG/TM) at NCI
http://medgen.ugent.be/rtprimerdb/index.php Ghent University ~3900 primer sets for multiple species, SG/TM
http://primerdepot.nci.nih.gov/    qPrimerDepot , mouse SG
http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome NCBI primer design and check website.

MicroRNA tools:
http://www.targetscan.org/   Website to search for miRNA targets.
http://cbio.mskcc.org/cgi-bin/mirnaviewer/mirnaviewer.pl Website to search for human miRNA targets.
http://pictar.bio.nyu.edu/ Website to search for miRNA targets.

UT Southwestern Medical Center resources:
Home to NIDDK-sponsored mouse metabolic phenotyping center (http://www.mmpc.org) directed by Craig Malloy and Shawn Burgess to use NMR to measure metabolic flux http://www2.swmed.edu/rogersmr/mouse/index.html
UT Southwestern Mouse Metabolic Core: http://www.utsouthwestern.edu/utsw/home/research/metstudcore/
Visualsonics VEVO770 small animal ultrasound (Ralph Mason): http://www.visualsonics.com/products/products_vevo770.htm
Seahorse extracellular flux (Scherer): http://www.bucher.ch/en/products/Seahorse_Bioscience/xf24-3_extracellular_flux_analyzer.html