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http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

•   Source: SciCrunch Registry

https://resistomedb.com

Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.

Proper citation: ResistomeDB (RRID:SCR_018305) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/%7Emarchini/software.html

An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)

Proper citation: POPGEN (RRID:SCR_007315) Copy   

•   Source: SciCrunch Registry

http://www.omicsexpress.com/sva.php

Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.

Proper citation: SVA (RRID:SCR_002155) Copy   

•   Source: SciCrunch Registry

http://courses.jax.org/2012/addiction.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.

Proper citation: Short Course on the Genetics of Addiction (RRID:SCR_005560) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/onemap/index.html

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/hapassoc/index.html

Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)

Proper citation: R/HAPASSOC (RRID:SCR_009365) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dgac/home/

Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center.

Proper citation: Stanford Diabetes Research Center Diabetes Genomics Analysis Core (RRID:SCR_016213) Copy   

•   Source: SciCrunch Registry

https://www.biotech.wisc.edu/services/gec

Core provides RNA library preparation services for Illumina, PacBio and Oxford Nanopore sequencing platforms. Single Cell RNA and Spatial Transcriptomics services are available with 10X Genomics technology. Provides RNA extraction, RNA QC and SNP genotyping and methylation bead array services. Provides support from project design through downstream analysis.Service facility, from hypothesis to publication.Microarray: expression and genotyping Affymetrix, Agilent, Nimblegen. Sequencing: RNA, gDNA, ChIP, Capture, 16SNovaSeq, HiSeq 2500, 3000, MiSeq.

Proper citation: Wisconsin-Madison University Biotechnology Center Gene Expression Center Core Facility (RRID:SCR_017757) Copy   

•   Source: SciCrunch Registry

https://www.umassmed.edu/tkomouse/

Core to produce genetically modified mice, rats, and stem cells for the UMMS Scientific Community.Composed of two facilities: Animal Modeling Facility and Gene Targeting and Stem Cell Facility.

Proper citation: Massachusetts University Medical School Transgenic Animal Modeling Core Facility (RRID:SCR_017729) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/microarray/

Core provides analysis of gene expression using Affymetrix GeneChip platform. Offers next generation sequencing via Illumina NextSeq and Ion Torrent PGM and Proton instruments, analysis of RNA and DNA using Agilent Bioanalyzer.

Proper citation: Boston University Microarray and Sequencing Resource Core Facility (RRID:SCR_017782) Copy   

•   Source: SciCrunch Registry

http://www.unmc.edu/ecf/

Core assists with epigenetic analysis including DNA Methylation, Chromatin Immunoprecipitation and Real Time Quantitative PCR gene expression analysis. Services include DNA Methylation Analysis, Specific Genomic Location Analysis:Methylation Specific PCR,Bisulfite Sequencing,Bisulfite Pyrosequencing,Qiagen PyroMark Pyrosequencer Instrumentation;Genome Wide Analysis:High Throughput Sequencing Methylation Analysis, Methyl-Sensitive Cut Counting (MSCC),Methyl CpG Binding Domain - Isolated Genome Sequencing (MiGS);Chromatin Immunoprecipitation Analysis (ChIP):Analysis of Histone Modifications,DNA-Protein Interactions,Chromatin Positions analyzed using:Quantitative PCR Analysis (Real-Time QPCR),High Throughput Sequencing Analysis (ChIP-Seq);Gene Expression Analysis (QPCR):Real-Time Quantitative PCR Gene Expression.

Proper citation: Nebraska University Medical Center Epigenomics Core Facility (RRID:SCR_017800) Copy   

•   Source: SciCrunch Registry

http://sites.northwestern.edu/stemcell/

Core provides iPSC technology services.Specialize in creating custom patient-derived iPSCs, providing training in stem cell culture, project consultation, CRISPR gene editing services, cell banking, and facility usage.

Proper citation: Northwestern University Stem Cell Core Facility (RRID:SCR_017873) Copy   

•   Source: SciCrunch Registry

http://www.garvan.org.au/research/capabilities/molecular-genetics

Core facility for high throughput services covering the areas of Capillary Sequencing, Mouse Genotyping, SNP Genotyping, Clinical Diagnostic Sequencing, Cell Line Identification, Gene Expression Analysis and DNA/RNA extraction.

Proper citation: Garvan Institute of Medical Research Molecular Genetics Core Facility (RRID:SCR_017849) Copy   

•   Source: SciCrunch Registry

http://hihg.med.miami.edu/cgt/gene-expression

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip.

Proper citation: University of Miami Miller School of Medicine Gene Expression Core Facility (RRID:SCR_017825) Copy   

•   Source: SciCrunch Registry

https://cri.utsw.edu/facilities/mouse-genome-engineering-core/

Core provides production of mouse models to support fundamental and translational research. Provides transgenic, gene targeting,DNA microinjection services, CRISPR/Cas9 microinjection, ES cell manipulation and other microinjection services to generate transgenic mice, knock-in/knock-out mice and chimeric mice harboring select genetic mutations. Other services include mouse sperm cryopreservation and recovery, in vitro fertilization (IVF), rederivation of pathogen free mouse lines and derivation of mouse embryonic stem cell lines. Provides general consultations on experimental designs and vectors for gene modification-related projects, DNA preparation, recombinant ES clones, mouse genotyping, colony breeding and husbandry, customize services as requested to support development of animal models for modeling human diseases.

Proper citation: University of Texas Southwestern Medical Center Mouse Genome Engineering Core Facility (RRID:SCR_017921) Copy   

•   Source: SciCrunch Registry

https://ccb-compute.cs.uni-saarland.de/mirtargetlink2/

Web application provides users with visualization interface to explore and analyze interaction networks between miRNAs and target genes.

Proper citation: miRTargetLink (RRID:SCR_026858) Copy   

•   Source: SciCrunch Registry