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Molecular Biology Resource

Director: Sanchez, Yolanda

Summary:

This core facility provides molecular biology products, services, and support to help investigators solve their basic, translational, and clinical research problems. Our services include DNA fragment analysis, qPCR, Sanger sequencing and NanoString Technology. It is our goal to offer the highest quality products and services possible in the most cost effective manner.

Affiliations:

People:

Resources:

Instruments

  • ABI 3730 DNA analyzer ( DNA sequencer )

    "The 48-capillary 3730 DNA Analyzer is the Gold Standard in medium-to-high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample. This is upgradeable to 96 capillaries."

  • ABI GeneAmp PCR System 2700 ( Thermal cycler )

    "The GeneAmp PCR System 2700 is an automated instrument, specifically designed for the amplification of nucleic acids using the GeneAmp Polymerase Chain Reaction (PCR) process.

    The instrument has an integrated 96-well sample block, which houses an internal Peltier heating/cooling unit. The sample block is made of aluminum to provide optimal thermal transfer rate."

  • NanoString nCounter Gene Expression System ( Cell assay platform )

    The nCounter Analysis System will perform:
    Single Cell Gene Expression Analysis,
    miRNA Expression Analysis,
    miRGE Analysis, Copy Number Variation Analysis,
    lncRNA Expression Analysis,
    ChIP Expression Analysis and
    Leukemia Fusion Gene Analysis. The next generation (GEN2) of the advanced nCounter Analysis System delivers the same reproducible results from a wide range of sample types with enhanced features that include a higher throughput, an improved user-interface, and a smaller footprint. The system is designed and manufactured under GMP/ISO 13485 and its innovative design provides improved reliability.

    The nCounter Prep Station is the automated liquid handling component of the nCounter Analysis System. It processes samples post-hybridization to prepare them for data collection on the nCounter Digital Analyzer. Prior to placing samples on the Prep Station, samples are hybridized according to the nCounter protocol. On the deck of the Prep Station, hybridized samples are purified and subsequently immobilized in the sample cartridge for data collection.

    All consumable components and reagents required for sample processing on the Prep Station are provided in the nCounter Master Kit and arrive in your lab ready to load on the deck of the robot. The Prep Station can process up to 48 samples in a 10-hour time span.

    The nCounter Digital Analyzer collects data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the data output files include the target identifier and count number along with a comprehensive tally of internal controls that allows each assay to be quantitative. The small data files can be distributed using a variety of methods and are easily integrated with commonly used data analysis and visualization packages.

    The nCounter Gene Expression Assay is designed to provide an ultra-sensitive, reproducible and highly multiplexed method for detecting gene expression across all levels of biological expression. This assay provides a method for direct detection of mRNAs with molecular barcodes called nCounter Reporter Probes without the use of reverse transcription or amplification.

  • PerkinElmer Janus Workstation ( Liquid handling system )

    8 tip station

Protocols

Services

  • DNA fragment analysis ( Material analysis service )

    "The MB&P Core laboratory is equipped with two ABI Model 3100 genetic analyzers, which are routinely used for our standard DNA sequencing service. However, the instruments can also be used for a number of popular genetic assays based on DNA fragment (size) analysis. These assays include microsatellite, SNP, and AFLP analysis. The instruments allow multiplexing of the assays and use fifth dye technology; four reporter dyes and a fifth dye for standards in a single capillary. The core facility staff will be glad to assist in planning experiments using this technique. For more information contact the Core Facility."

  • DNA sequencing service ( Material analysis service )

    "The laboratory is equipped with two ABI Model 3100 genetic analyzers, routinely used for our standard DNA sequencing service. These instruments avail themselves to several different DNA sequencing techniques featuring longer reads and shorter run times that may be useful for specific projects. The instruments can also be used for a number of popular genetic assays based on DNA fragment (size) analysis. The core facility staff will be glad to assist in planning experiments using these instruments."

  • Genotyping service ( Material production service )

    Purify DNA from ES clones (to screen for targeted clones) or tail biopsies (to screen for founders or transgenic offspring). Establish a genotype assay if not already established. Genotype by PCR or Southern blot.

Software

  • 3730 DNA Analysis Data Collection ( Software )

  • ABI DNA Sequencing Analysis Software ( Software )

    "This software enables you to basecall, trim, display, edit, and print data from our entire line of capillary DNA sequencing instruments for data analysis and quality control."

  • ABI Peak Scanner ( Software )

    "Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers."

  • FinchTV ( Software )

    "Geospiza’s FinchTV is the popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces."

  • GeneMapper ( Software )

    "GeneMapper® Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems.

    This software specializes in multiapplication functionality, including amplified fragment length polymorphism (AFLP®), loss of heterozygosity (LOH), microsatellite, and SNP genotyping analysis.

    GeneMapper® Software can help users increase data processing efficiency with remote auto-analysis and command line operation, and allows for multiuser, client-server deployment.

    The software uses Process Quality Values (PQVs) for automated identification that reduces data review time for high throughput genotyping. In addition, the security and audit features help users meet 21 CFR 11 requirements."

  • Sequence Scanner ( Software )

    "The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. The software generates graphically expressive reports on results."

  • Variant Reporter ( Software )

    "The Variant Reporter® Software performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation. The robust algorithms will call SNPs, mutations, insertions, deletion and heterozygous insertions/deletions for data generated using the Applied Biosystems Genetic Analyzers."


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Last updated: 2014-06-09T12:36:14.752-04:00

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