The ultimate goal of the JAX 4D Nucleome Center is to deliver a Nucleome Positioning System (NPS) for the generation of complex maps of chromatin interaction network in the context of 3D genome structures.
Alzheimer’s disease (AD) is a major cause of dementia, disability and death in the elderly. Despite recent advances in our understanding of basic biological mechanisms underlying AD, we do not yet know how to prevent AD or have an approved disease modifying intervention.
NOD-scid IL2rgnull (NSG) and NOD-Rag1null IL2rgnull (NRG) mice support heightened levels of engraftment with human cells and tissues. These engrafted mice allow research on human disease processes without putting individuals at risk.
One of the key challenges in cancer treatment is to overcome the primary resistance of any tumor to the emerging range of treatments.
The Jackson Laboratory maintains and distributes chromosome-aberration stocks that provide mouse models for Down syndrome, as well as the study of chromosomal aneuploidy.
Resource lists and describes mouse models for ocular research at JAX.
This Strain Survey GEM holds data for a gene expression survey of 26 inbred mouse strains. Users can perform simple or advanced queries to find various locations of interest.
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases.
Allows users to integrate gene sets across species, tissue and experimental platform.
Genetic Resource Science initiates and develops resource-generating research. Our team: identifies and implements innovative technologies for genetic research; makes and distributes new mouse models; and provides extensive genetic and phenotypic information on JAX mouse strains.
Online tool used to find genes and transcripts in designated regions. Users can either enter a range manually or click and drag to select a region of interest.
This theme takes a broad approach to instability, examining oncogenic processes that restructure the genome and translate it to the specified regulatory and protein outputs that reprogram the cancer cell.
This software is used to fit Hidden Markov Models in Stochastic models for heterogeneous DNA sequences.
Integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
ATAC-seq is a new protocol to capture open chromatin sites by performing adaptor ligation and fragmentation of open chromatin regions. Due to its efficiency in requirement of biological sample and in library preparation time, many scientists are generating ATAC-seq libraries to decipher the chromatin landscape of DNA in a given cell type and condition of interest.
The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains.
J/maanova is an open sourced desktop application developed with the aim of simplifying the analysis of microarray experiments.
J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.
To understand disease mechanisms and ultimately develop effective therapies for AD, it is essential we apply state-of-the-art approaches to generate the next generation of more predictive animal models and make these models widely available to the AD research community.
The Jackson Laboratory Cancer Center (JAXCC) is a National Cancer Institute-designated Cancer Center complemented by institutional education, resource and service initiatives that support cancer research world-wide. The NCI designated JAXCC comprises approximately 50 members with multidisciplinary expertise who are united in research aimed at understanding and targeting the genomic complexity of cancer.
The JAX Cre Repository's aim is to provide the scientific community with a centralized, comprehensive set of well-characterized Cre-driver lines and related information resources.
Scientists in the JAX Center for Genetics of Fertility and Reproduction work on a variety of scientific problems of relevance to fertility and newborn health.
The goal of the CGD is to evaluate the role of genome-wide organization in mammalian biology by developing detailed maps of genetic interactions that encompass allelic diversity, functional categories, gene expression, recombination hotspots, and phenotype associations.
In this project we will create mice carrying the human pathogenic mutations identified by our collaborators. The mutations will be introduced onto both a standard, stable genetic background (C57BL/6J strain) and, to better emulate the human situation, onto a highly diverse genetic background (Diversity Outcross (DO) mice). The resulting new mouse models will be utilized to recapitulate and study key features of ALS pathophysiology. Successful models will be used to test drugs already approved by the FDA as well as to develop new drugs tailored to specific mechanisms of action and the impaired biological pathways of the mutated genes.
The JAX Colony Management System (JCMS) is a free and supported multi-user relational database system for managing research mouse colonies.
Our specialized collection areas include: genetics, inbred mice, animal health and husbandry, development, embryology, complex traits, immunology, cancer, molecular biology, neuroscience and computational biology.
Scientists around the world are working to generate a targeted knockout mutation for every gene in the mouse genome through the Knockout Mouse Project (KOMP) which is providing critical tools for understanding gene function and the genetic causes of human diseases.
MAANOVA is a set of functions written in Matlab for the analysis of variance on microarray data.
These programs are based on marker regression and are designed for detecting covariate effects and interactions from inbred line cross data.
MAV-seq (Management, Analysis, Visualization of Sequence data) is an interactive, user friendly, cross platform, secure, encrypted, automated, customized, centralized, multi-roles based database application for the management of sample repertoires and automation of the data pre-processing of epigenomic and transcriptomic data.
MoDIS links to the Pathbase.net website to provide detailed information and annotated images of similar lesions in laboratory mice, making it a unique and useful training aid.
International database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data.
Mice harboring spontaneous mutations have long been a major source for animal models of human genetic disorders, particularly mendelian diseases. The Mouse Mutant Resource maintains over 700 established mutant strains.
This resource is a collaborative standardized collection of measured data on laboratory mouse strains and populations. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect. Also includes protocols, projects and publications, and SNP, variation and gene expression studies.
Custom genome browser provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains.
This resource provides mouse models for facial, dental, eye, ear and skull development research, as well as mouse models of human craniofacial syndromes.
The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by electronic access to a variety of information.
MouseCyc is a new, manually curated database of both known and predicted metabolic pathways for the laboratory mouse. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways, 1,790 enzymatic reactions, and 1,122 compounds in MouseCyc.
The Mutant Mouse Resource and Research Center (MMRRC) distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community.
Our goal is to focus our diverse expertise in biology and genomics on the problems and disorders associated with aging.
For over half a century Oak Ridge National Laboratory generated and maintained a diverse collection of mouse stocks. A large part of this collection derived from induced mutagenesis programs using radiation or chemical mutagens. Many of these mutant stocks were cryopreserved at the Oak Ridge facility. In 2009 The Jackson Laboratory accepted and agreed to distribute the cryopreserved embryos and sperm in order that this resource would continue to be available to the worldwide research community.
OncoCL, an ontology to describe cancer cell types
We offer a growing number of mouse lines expressing proteins that activate, inhibit or detect neuronal activity.
The Parkinson’s Disease Mouse Model Resource characterizes and distributes new mouse models of Parkinsonism and Parkinson’s disease.
Serves as a centralized resource for mouse models and tools that have been validated for use in preclinical studies of peripheral neuropathy.
Research in this area seeks to define the genomic parameters of cancer progenitors, use these systems to understand the root cause of certain cancers, reconstruct cancer states in primary cells using systems approaches, and provide "intelligent" combinatorial therapeutics.
Pseudomarker is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses.
PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser.
70+ QTL studies in a number of research areas, gathered and curated by the Churchill Group QTL Archive initiative.Each QTL study has phenotype and genotype data for members of a population derived from a specific cross.
QuIN (Query tool for Interaction Networks, available at quin.jax.org) is a tool for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC.
R/maanova is an extensible, interactive environment for Microarray analysis.
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.
350 million people are affected by rare and orphan disease. The Rare and Orphan Disease Center conducts research to better treat these diseases.
Produce and distribute mutant models for infertility and to investigate underlying causes in order to identify new genes and pathways contributing to reproductive function.
Random Forest Regression for Epigenetic Length prediction
Interested in a career at The Jackson Laboratory? We empower and accelerate JAX research and discoveries with a broad array of shared scientific services and facilities.
SeqFold is a tool for RNA secondary structure prediction from experimental data.
High quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources.
The SMSR maintains mice that are important tools for genetic analysis of complex diseases, including consomic strains.
We collect, cryopreserve and distribute mouse strains important to research in type 1 diabetes.