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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

http://www.scienceexchange.com/facilities/university-of-utah

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Labs and facilities of the University of Utah, which include: Microarray and Genomic Analysis Core Facility, Flow Cytometry Core Facility, Mutation Generation and Detection Facility, and the Transgenic and Gene Targeting Core.

Proper citation: University of Utah Labs and Facilities (RRID:SCR_001042) Copy   

•   Source: SciCrunch Registry

http://archive.ics.uci.edu/ml/datasets/EEG+Database

Data set from a large study to examine EEG correlates of genetic predisposition to alcoholism. It contains measurements from 64 electrodes placed on the scalp sampled at 256 Hz (3.9-msec epoch) for 1 second. There were two groups of subjects: alcoholic and control. Each subject was exposed to either a single stimulus (S1) or to two stimuli (S1 and S2) which were pictures of objects chosen from the 1980 Snodgrass and Vanderwart picture set. When two stimuli were shown, they were presented in either a matched condition where S1 was identical to S2 or in a non-matched condition where S1 differed from S2. There were 122 subjects and each subject completed 120 trials where different stimuli were shown. The electrode positions were located at standard sites (Standard Electrode Position Nomenclature, American Electroencephalographic Association 1990). Zhang et al. (1995) describes in detail the data collection process. There are three versions of the EEG data set. * The Small Data Set (smni97_eeg_data.tar.gz) contains data for the 2 subjects, alcoholic a_co2a0000364 and control c_co2c0000337. For each of the 3 matching paradigms, c_1 (one presentation only), c_m (match to previous presentation) and c_n (no-match to previous presentation), 10 runs are shown. * The Large Data Set (SMNI_CMI_TRAIN.tar.gz and SMNI_CMI_TEST.tar.gz) contains data for 10 alcoholic and 10 control subjects, with 10 runs per subject per paradigm. The test data used the same 10 alcoholic and 10 control subjects as with the training data, but with 10 out-of-sample runs per subject per paradigm. * The Full Data Set contains all 120 trials for 122 subjects. The entire set of data is about 700 MBytes.

Proper citation: EEG Database (RRID:SCR_001581) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/genomes

The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins

Proper citation: EBI Genomes (RRID:SCR_002426) Copy   

•   Source: SciCrunch Registry

https://clinicaltrials.gov/study/NCT00342927?term=AREA%5BBasicSearch%5D(NIDDK%20endocrine%20and%20diabetes)%20AND%20AREA%5BSponsorSearch%5D(NIDDK)%20AND%20AREA%5BOverallStatus%5D(NOT_YET_RECRUITING%20OR%20RECRUITING%20OR%20ACTIVE_NOT_RECRUITING)&rank=1

Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease

Proper citation: Family Investigation of Nephropathy of Diabetes (RRID:SCR_001525) Copy   

•   Source: SciCrunch Registry

http://bpg.utoledo.edu/~afedorov/lab/eid.html

Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

Proper citation: EID: Exon-Intron Database (RRID:SCR_002469) 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

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://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

http://www.uoguelph.ca/~rdanzman/software/PROBMAX/

Software application for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny (entry from Genetic Analysis Software)

Proper citation: PROBMAX (RRID:SCR_009337) Copy   

•   Source: SciCrunch Registry

http://www.statgen.ucr.edu/software.html

Software application that is a user defined SAS procedure for mapping quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, it can be called just like any other SAS procedures. Users will not notice the differences between this customized procedure and other built-in SAS procedures. (entry from Genetic Analysis Software)

Proper citation: PROC QTL (RRID:SCR_009338) Copy   

•   Source: SciCrunch Registry

http://phg.mc.vanderbilt.edu/content/powertrim

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software)

Proper citation: POWERTRIM (RRID:SCR_009333) Copy   

•   Source: SciCrunch Registry

http://ftp://statgen.ncsu.edu/pub/zaykin/

Software application performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination. (entry from Genetic Analysis Software)

Proper citation: MLD (RRID:SCR_009298) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)

Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)

Proper citation: MLBGH (RRID:SCR_009297) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html (in Russian)

Software program for analysis of mitochondrial diseases (entry from Genetic Analysis Software)

Proper citation: MITPENE (RRID:SCR_009294) Copy   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: MKGST (RRID:SCR_009295) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Minimac

Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)

Proper citation: MINIMAC (RRID:SCR_009292) Copy   

•   Source: SciCrunch Registry