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http://www.bios.unc.edu/~lin/software/MAOS/

Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)

Proper citation: MAOS (RRID:SCR_013351) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/alien-hunter

Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.

Proper citation: Alien-hunter (RRID:SCR_015967) Copy   

•   Source: SciCrunch Registry

http://www.lji.org/faculty-research/scientific-cores/functional-genomics/#overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5, 2024. Core facility that combines large-scale automation and high-throughput capabilities with gene disruption techniques to pinpoint the function of individual genes and find new ways to disrupt genetic triggers of disease. The research capabilities are aimed towards finding new treatments for immune-related diseases.

Proper citation: La Jolla Institute for Allergy and Immunology Functional Genomics Core Facility (RRID:SCR_014836) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/vcr/cores/vcr-cores/mgec/index.html

Core Facility provides expertise and advice for experimental design of transgenic or gene knockout experiments, including DNA construct production and genotyping assays, makes reagents available for generation of transgene or gene targeting constructs, and performs all experimental aspects, which include pronuclear injection of transgene constructs, generation of recombinant mouse ES cells, blastocyst injection, and embryo transfer surgeries, for generation or rederivation of genetically manipulated mouse strains. Transgenic founder mice or chimeric animals with targeted alleles are then transferred to individual investigator for analysis.

Proper citation: Nebraska University Medical Center Mouse Genome Engineering Core Facility (RRID:SCR_017755) Copy   

•   Source: SciCrunch Registry

http://einstein.yu.edu/shRNA

Core Facility was closed in November 2016. Services of shRNA Core were redistibuted to other existing facilities at Einstein.Gene Modulation Services: CRISPR, RNAi and ORF. CRISPR-Cas9 services for cell lines will now be performed in Gene Modification Facility. Gene Modification Facility already offers CRISPR services for genetic modification of mice and will utilize this scientific expertise to provide CRISPR services for the gene modification of cell lines as well. You can access these services through core's site in iLab.The human and mouse whole genome shRNA library has been relocated to the Molecular Cytogenetic Core. The core staff will pull requested shRNA and ORF clones from our collection for investigators. You can access this service through the core's site in iLab.Access and operation of the Operetta instrument for high-content imaging will now be coordinated through the Macromolecular Therapeutics Development Facility (MTDF). You can access this service through the core's site in iLab. Lentivirus prep from shRNA and CRSPR constructs can be obtained from our Gene Therapy Core from clones obtained from the Molecular Cytogenetic Core. You can access this service through the core's site in iLab.

Proper citation: Albert Einstein College of Medicine shRNA Core Facility (RRID:SCR_017846) Copy   

•   Source: SciCrunch Registry

https://ki.mit.edu/sbc/escell

Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells.

Proper citation: Massachusetts Institute of Technology Koch Institute Preclinical Modeling Core Facility (RRID:SCR_017899) Copy   

•   Source: SciCrunch Registry

http://ssom.luc.edu/genomics/

Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths.

Proper citation: Loyola University Genomics Core Facility (RRID:SCR_017857) Copy   

•   Source: SciCrunch Registry

http://www.uwtransgenics.org/

Core facility that creates transgenic and gene-targeted mice using pronuclear microinjection, targeted ES cell microinjection, and CRISPR/Cas9 gene editing. Offers mouse rederivation services to create specific pathogen free mice or to rederive cryopreserved mouse lines. Additionally, embryo and sperm cryopreservation services are available to provide long-term storage of valuable mouse strains or stocks. Services include:Pronuclear Microinjection,ES Cell Microinjection,ES Cell Electroporation CRISPR/Cas9,In Vitro Fertilization,Sperm Cryopreservation,Embryo Cryo,Embryo Rederivation.

Proper citation: University of Washington Transgenic Resources Program Core Facility (RRID:SCR_017863) Copy   

•   Source: SciCrunch Registry

http://exac.broadinstitute.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. An aggregated data platform for genome sequencing data created by a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data set provided on this website spans 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies. They have removed individuals affected by severe pediatric disease, so this data set should serve as a useful reference set of allele frequencies for severe disease studies. All of the raw data from these projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. They ask that you not publish global (genome-wide) analyses of these data until after the ExAC flagship paper has been published, estimated to be in early 2015. If you''re uncertain which category your analyses fall into, please email them. The aggregation and release of summary data from the exomes collected by the Exome Aggregation Consortium has been approved by the Partners IRB (protocol 2013P001477, Genomic approaches to gene discovery in rare neuromuscular diseases).

Proper citation: ExAc (RRID:SCR_004068) Copy   

•   Source: SciCrunch Registry

http://channelpedia.epfl.ch/

An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed.

Proper citation: ChannelPedia (RRID:SCR_003807) Copy   

•   Source: SciCrunch Registry

http://www.inmex.ca./INMEX/

A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

Proper citation: INMEX (RRID:SCR_004173) Copy   

•   Source: SciCrunch Registry

http://www.flytf.org/

A database of genomic and protein data for Drosophila site-specific transcription factors.

Proper citation: FlyTF.org (RRID:SCR_004123) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-4/search?q=*

Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).

Proper citation: Integrated Brain Gene Expression (RRID:SCR_004197) Copy   

•   Source: SciCrunch Registry

http://www.nephromine.org/

THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.

Proper citation: Nephromine (RRID:SCR_003813) Copy   

•   Source: SciCrunch Registry

http://life.ccs.miami.edu/life/

LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal.

Proper citation: LINCS Information Framework (RRID:SCR_003937) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mmgp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database providing access and limited analysis to the MMGP portal data sets. These include the MMRC funded reference array comparative genomic hybridization (aCGH) and gene expression data and additional public multiple myeloma datasets. The MMGP will be updated with new features such as additional data and analysis tools as they become available.

Proper citation: Multiple Myeloma Genomics Portal (RRID:SCR_003722) Copy   

•   Source: SciCrunch Registry

http://www.hgsc.bcm.tmc.edu/content/hapmap-3-and-encode-3

Draft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site.

Proper citation: HapMap 3 and ENCODE 3 (RRID:SCR_004563) Copy   

•   Source: SciCrunch Registry

http://integromedb.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds.

Proper citation: IntegromeDB (RRID:SCR_004620) Copy   

•   Source: SciCrunch Registry

http://www.yeastgenome.org/

A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.

Proper citation: SGD (RRID:SCR_004694) Copy   

•   Source: SciCrunch Registry