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http://www.sanger.ac.uk/science/tools/dindel

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Proper citation: DINDEL (RRID:SCR_001827) Copy   

•   Source: SciCrunch Registry

http://solar-eclipse-genetics.org

A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software)

Proper citation: SOLAR (RRID:SCR_000850) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~gqian/software.htm (not available)

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MRH (RRID:SCR_000841) Copy   

•   Source: SciCrunch Registry

http://www.biosciences-labs.bham.ac.uk/Kearsey/

Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software)

Proper citation: QTL CAFE (RRID:SCR_000844) Copy   

•   Source: SciCrunch Registry

http://casestudies.brain-map.org/celltax

Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.

Proper citation: CellTax vignette (RRID:SCR_017000) 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

https://www.pharmaron.com/

Contract Research, Development, and Manufacturing Organization (CRDMO) supporting the life sciences industry. Founded in 2004, it provides comprehensive services for small molecules, biologics, and cell and gene therapies (CGT) from discovery to commercialization. Offers integrated R&D, laboratory services, and manufacturing.

Proper citation: Pharmaron (RRID:SCR_028035) Copy   

•   Source: SciCrunch Registry