Table II.
Enabling Technologies and Resources
| General Resource for Data and Resources | ||
| Neuroscience Information Framework | A web portal and search engine that links to data and research resources and has the capability of searching data and resources in the hidden web. | http://neuinfo.org |
| Genetic Resources for Rat and Mouse | ||
| Mouse Genome Informatics Database | International database of biological resources for the mouse. | www.informatics.jax.org |
| Genenetwork | GeneNetwork is a database and open source bioinformatics software resource for systems genetics | www.genenetwork.org |
| Geneweaver | Gene Weaver allows users to integrate phenotype centered gene sets across species, tissue and experimental platform | http://geneweaver.org/ |
| Mouse Phenome Database | Collaborative collection of baseline phenotypic data on inbred mouse strains | http://phenome.jax.org |
| International Mouse Phenotyping Consortium (IMPC) | Phenotype and characterize the function of 20,000 known and predicted mouse genes | http://www.mousephenotype.org/ |
| The Rat Genome Database | Genetic resources for rat | http://rgd.mcw.edu/ |
| Rat Resource and Research Center | A NIH-funded Resource Center to supply biomedical investigators with the rat models, embryonic stem cells, related reagents, and protocols they require for their research. | http://www.rrrc.us/ |
| Resources for Knockout Mice | ||
| International Gene Trap Consortium (IGTC) | IGTC represents all publicly available gene trap cell lines, which are available on a non-collaborative basis for nominal handling fees. | http://www.genetrap.org/ |
| International Knockout Mouse Consortium | Knockout Mouse Project (KMP, funded by NIH) European Conditional Mouse Mutagenesis Project (EUCOMM, funded by European Union) North American Conditional Mouse Mutagenesis Project (NorCOMM, funded by Genome Canada) Texas A&M Institute for Genomic Medicine (TIGM) |
www.knockoutmouse.org |
| Mutant Mouse Regional Resource Centers (MMRRCs) | Distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community. | http://www.mmrrc.org/about/generalInfo.php |
| International Mouse Strain Resource (IMSR) | A searchable database of mouse strains, stocks, and mutant ES cells that are available in public repositories | www.findmice.org |
| Cre-Driver and FLP-Driver Lines | ||
| Cre-driver Network | Database and Expression profile of Cre driver lines supported by the NIH Blueprint | www.credrivermice.org |
| The Jackson Laboratory Cre Repository | Provides the scientific community information about a comprehensive set of well characterized Cre driver lines and their availability | http://cre.jax.org/index |
| The Jackson Laboratory FLPe repository | Provides information about available FLP-FRT recombinases in mice and constructs | http://www.jax.org/search/Main.jsp?qt=Research+tools+FLP-FRT+System&sg=0 |
| Cre-X-Mice: A database of Cre Transgenic Lines | A database of Cre-transgenic lines maintained by Andras Nagy at Mt Sinai Hospital, Toronto, Canada | http://nagy.mshri.on.ca/cre_new/index.php |
| Allen Brain Atlas expression map of Cre and other drivers | Expression maps of transgenic Cre and other driver lines in mice | http://connectivity.brain-map.org/transgenic/search/basic/ |
| Gensat Cre-Mice | Provides tissue specific expression of Cre recombinases expressed in Bacterial Artificial Chromosomes | http://www.gensat.org/cre.jsp |
| Full Length cDNAs | ||
| Mammalian Gene Collection (MGC) | Full length cDNAs for human, mouse, rat, and cow | http://mgc.nci.nih.gov/ |
| The Xenopus Gene Collection | Full length cDNAs for Xenopus | http://xgc.nci.nih.gov/ |
| The Zebrafish Gene Collection | Full length cDNAs for Zebrafish | http://zgc.nci.nih.gov/ |
| Viral Vectors | ||
| National Gene Vector Biorepository (NGVB) | A NIH-funded Center to address the increasing needs of the research community for access to the use of viral transneuronal tracing tracers. This approach is the most widely used method to gain a circuit perspective on the functional architecture of the nervous system at a cellular level. | https://www.ngvbcc.org/Home.action |
| Tissue-Specific Enhancers and Promoters | ||
| Pleiades Promoter Project: | This resource provides mini-promoters to drive tissue specific expression. | http://www.pleiades.org/ |
| The ENCODE Project | Then ENCyclopedia Of DNA Elements provides information about the functional elements in the genome | http://www.genome.gov/10005107 |
| Genome Browsers | ||
| University of California at Santa Cruz Genome Browser | Provides reference sequences and working draft assemblies for large collection of genomes and access to the ENCODE and Neanderthal projects. | http://genome.cse.ucsc.edu/ |
| Ensembl Genome Browser | Produces genome database for the eukaryotic and vertebrate organisms. | http://www.ensembl.org/index.html |
| NCBI Genome | This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. | http://www.ncbi.nlm.nih.gov/genome |
| Epigenomes | ||
| NIH Roadmap Epigenomics Mapping Consortium | A consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility, and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. | http://www.roadmapepigenomics.org/ |
| The ENCODE Project | The ENCyclopedia Of DNA Elements provides information about the functional elements in the genome | http://www.genome.gov/10005107 |
| Epigenomics | Genome wide maps of DNA and chromatin modifications | http://www.ncbi.nlm.nih.gov/epigenomics/ |
| MicroRNA | ||
| microRNA.org | A website service to predict microRNA targets & target downregulation scores. Experimentally observed expression patterns. |
http://www.microrna.org/microrna/home.do http://www.rnainterference.org/(for background) |
| Proteins | ||
| NIF Antibody Registry | Provides a stable, traceable, permanent identifier to all antibody products created by large commercial vendors and individual | http://www.neuinfo.org/products/antibodyregistry/ |
| Protein Database | Databases of protein sequences and 3dimensional structures of proteins | http://www.ncbi.nlm.nih.gov/protein |
| Other Important Research Resources | ||
| Drosophila Genomics Resource Center (DGRC) | A NIH-funded Center which serves the Drosophila research community to provide services on DNA clones, cell lines, microarrays and the emerging genomics technologies. | https://dgrc.cgb.indiana.edu/ |
| Zebrafish International Resource Center | A NIH-funded Resource Center to provide a central repository for wild-type and mutant strains of zebrafish (Danio rerio) and for materials and information about zebrafish research. | http://zebrafish.org/zirc/home/guide.php |
| Model Organisms for Biomedical Research | Provides information about resources for model organisms | http://www.nih.gov/science/models/ |