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.
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.
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.
Describes mouse models for ocular research available at The Jackson Laboratory and provides a list of known mouse mutations that affect vision.
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.
The Parkinson’s Disease Mouse Model Resource characterizes and distributes new mouse models of Parkinsonism and Parkinson’s disease.
We offer a growing number of mouse lines expressing proteins that activate, inhibit or detect neuronal activity.
This resource provides mouse models for facial, dental, eye, ear and skull development research, as well as mouse models of human craniofacial syndromes.
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.
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases.
Our specialized collection areas include: genetics, inbred mice, animal health and husbandry, development, embryology, complex traits, immunology, cancer, molecular biology, neuroscience and computational biology.
The International Mouse Strain Resource offers users a combined catalog of worldwide mouse resources (live, cryopreserved, and embryonic stem cells), with direct access to repository sites holding those resources of interest.
The JAX Colony Management System (JCMS) is a free and supported multi-user relational database system for managing research mouse colonies.
The Mouse Models of Human Cancer Database (formerly, the Mouse Tumor Biology database) integrates data on the frequency, incidence, genetics, and pathology of neoplastic disorders, emphasizing data on tumors that develop characteristically in different genetically defined strains of mice.
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.
High quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources.
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.
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.
The SMSR maintains mice that are important tools for genetic analysis of complex diseases, including consomic strains.
The Jackson Laboratory maintains and distributes chromosome-aberration stocks that provide mouse models for Down syndrome, as well as the study of chromosomal aneuploidy.
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.
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.
The Cre Portal contains curated data about all recombinase-containing transgenes and knock-ins developed in mice to provide a comprehensive resource delineating known recombinase activity patterns and allowing users to find relevant mouse resources for their studies.
International database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data.
SeqFold is a tool for RNA secondary structure prediction from experimental data.
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.
Random Forest Regression for Epigenetic Length prediction
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.
Serves as a centralized resource for mouse models and tools that have been validated for use in preclinical studies of peripheral neuropathy.
Produce and distribute mutant models for infertility and to investigate underlying causes in order to identify new genes and pathways contributing to reproductive function.
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.
Computational Sciences supports computational approaches to complex problems; develops software applications and platforms that facilitate access, visualization and sharing of data and algorithms and support JAX's research data and service products.
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.
Integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
FusorSV is a data mining-based framework that allows for comprehensive and robust detection of Structural Variations (SV) from next generation sequencing datasets. We built SV engine (SVE) that includes all tools including fusorSV that can be used for analysis of new datasets. SVE also includes data models built using 1000 Genomes SV callsets as ground truth.
MouseMine is a powerful data warehouse providing comprehensive API (application programming interface) access to MGI data, as well as a forms-based user interface.
Tools for automatic glomerulus identification and histological quantification from scanned PAS slides
The WORM Human OrthoLogy Explorer is a meta-tool that uses machine learning to predict novel least diverged orthologs (LDOs) by integrating ortholog predictions from 17 algorithms.
This tool calculates the glomerular filtration rate in mice using the FITC-inulin method
Phenotype and RNAseq data from approx. 200 (B6-Col4a5 KO x DO)F1 mice
Human cancers and dog cancers have a surprising amount in common. At The Jackson Laboratory, we believe that by studying canine cancers, we can gain important insights that may benefit both species!
GeneWeaver is a platform for the integrative analysis of heterogeneous functional genomics data. It allows users to compare and contrast biological functions across multiple species based on the genes, gene products and variants associated with these functions in global functional genomics analyses.
Supplemental tables and figures,
PDXNet is an NCI-sponsored consortium that uses patient-derived xenografts to accelerate translational research for the broader research community. The Chuang lab has been co-leader of the Data Coordination Center for this consortium since 2017.
CloudNeo is a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data.
SARNAclust is a novel semi-automatic algorithm to identify RNA-protein binding motifs from immunoprecipitation data.
Explore and compare multiple annotated mouse genomes.
The AMP-AD Knowledge Portal is a platform to access data, analytical results and tools generated within the National Institute of Aging’s AD Translational Research Program. The majority of the content in the Portal is genomic data generated from human samples or experimental model systems. The Portal also contains analytical results and data summaries.
Model organism development and evaluation for late-onset Alzheimer's Disease.
Based on integrated analysis of paired-end RNA sequencing and DNA copy number data from The Cancer Genome Atlas(TCGA), The Tumor Fusion Gene Data Portal provides a bona-fide fusion list across many tumor types.
Interactive web-based analysis tool that will allow users to replicate analyses reported for a study.
The MMR mouse variation database provides access to all genetic variants called from high-throughput exome and whole genome sequencing from mice exhibiting spontaneously arising Mendelian disease phenotypes. Phenotype, genetic mapping, and variant frequency metrics are also provided. Aggregated data analyses provide mutation candidate prioritization.
Tool to quantify images where meaningful differences are discernible by eye, but difficult to quantify using traditional methods.
The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease.
A web application for performing haplotype analysis of genotype calls from the “MUGA” platform genotyping arrays
Visualize and interrogate gene expression changes in glaucoma
PDX Finder is an open global cancer research portal to patient derived xenograft (PDX) models.
Mouse Genome Database (MGD) is a core knowledgebase for the laboratory mouse and is focused on providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. MGD is a primary component of the Mouse Genome Informatics (MGI) Consortium.
Gene Expression Database (GXD) is a database project that integrates different types of gene expression information from the mouse and provides a searchable index of published experiments on endogenous gene expression during development. GXD as a core component of the Mouse Genome Informatics (MGI) resource which is the international community database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
sRACIPE is a systems-biology modeling method which takes the gene regulatory circuit topology as the only input, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises yielding new insights on the structure and function of gene regulatory networks.
An R package for eQTL/pQTL mediation analysis.
Genotype-free genome reconstruction and ASE quantification.
Genome Editing tools. Creates custom genomes by incorporating (phased) SNPs and indels into reference genome, extracts regions of interest, e.g., exons or transcripts, from custom genomes, and converts coordinates of files (bam, gtf, bed) between two genomes.
CKB is a dynamic, digital encyclopedia for precision oncology that connects cancer variants to therapies, efficacy evidence, and clinical trials and aids interpretation of complex cancer genomic profiles.
An expectation maximization algorithm for allele specific expression. Primary author K. Choi of the Churchill Lab.
Processes NGS alignments into a sparse compressed incidence matrix. Stores pre-defined binary format for efficient downstream analyses and storage.
Application of deep neural networks to rigorously and reproducibly quantify complex properties of histological images.
The Center for Biometric Analysis (CBA) is a state-of-the-art, ~21,000-ft dedicated facility providing scientists with extensive facilities and expertise to perform in vivo mouse phenotyping, i.e., observation and measurement of mouse characteristics, spanning a broad range of biological domains and disease states.