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DNA Sequence Analysis Shared Resource

Summary:

We perform DNA sequencing & genomic analysis and RNA/DNA (oligonucleotide) synthesis on a fee-for-service basis. We are happy to consult on your sequence assembly and analysis or other data processing, informatics, and database needs as well.

People:

Resources:

Instruments

Protocols

  • Nucleic acid sample preparation for sequencing protocol ( Protocol )

    "You can really save some money by doing the cycle sequencing reactions yourself. Note that this does include cleaning up the labeled extension products prior to submitting them for the 3130xl.

    This mode is appropriate for very experienced clients with proven sample preparation systems and high-throughput needs. D-mode is not for samples that require troubleshooting, additional reagents, special cycling, data processing or analysis: use B-mode for those." See website for details.

    Protocols specific for:
    * Single tube samples
    * Samples in 96 well plate(s)

Reagents

Services

  • Bioinformatics integration of genomics datasets ( Data analysis service )

  • Bioinformatics software tools and analysis ( Data analysis service )

    "We offer free sequence assembly and primer design.

    We can also help with database development, data processing & automation programming (aka "Data Munging") and batch processing. On-going projects can be either collaborative or fee-for-service.

    If you find yourself cutting and pasting lots of data, or searching through long blast or other reports by hand, I can write scripts to automate the process and generate a spreadsheet or set of database records with the extracted bits."

    Service available to both internal and external investigators. See lab website for fee information.

  • DNA sequence sample preparation service ( Material production service )

    Five DNA sequence sample preparation services are available and they are as follows:
    * "A-mode is most appropriate for new clients, clients with few samples, new projects, and troublesome templates. We take your template and use either your custom primer or one of our common primers and give you an edited sequence data file ready for use."

    * "B-mode is most appropriate for clients seeking high priority, accurate sequencing, and ready to use sequencing data. It is economical, but does requires some skill with purification and quantification of template DNA."

    * "C-mode is most appropriate for those clients who want to save some money but are experienced clients with proven sample preparation systems, and easy to sequence templates. Sample preparation is the same as for B-mode samples, but you edit your own sequence data."

    * D-mode "is appropriate for experienced clients with proven sample preparation systems and high-throughput needs. D-mode is not for samples that require troubleshooting, additional reagents, special cycling, data processing or analysis: use B-mode for those."

    * E-mode is sample preparation for fragment analysis. The sample preparation is for fragment generation using your favorite protocol. Unincorporated nucleotides, primers, and salts are removed from the fragments."

  • DNA synthesis service ( Material production service )

  • Microsatellite genotyping service ( Material analysis service )

  • Mutation detection service ( Material analysis service )

  • Nucleic acid fragment analysis ( Material analysis service )

    "* Perform fragment generation for using your favorite protocol.
    * Clean up fragments to remove unincorporated nucleotides, primers, and salts.
    * Final sample concentration must be at 200ng in 1uL; If multiplexing, samples must also be at 200ng in 1uL.

    The maximum volume in each tube or well can ONLY BE 8uL (ex: If using G5, you can use the four dyes available twice, as long as the expected alleles vary in size. This would give a maximum value of 8uL. If you are unsure about how this works or would like to try other combinations please speak with us.)"

    We currently use:
    Dye Set: 6-FAM (blue), HEX (green), NED (yellow), ROX (red)
    Dye Set G5-DS-33: 6-FAM (blue), VIC (green)), NED (yellow), PET (red), LIZ (orange)
    We use GS500 (-250) LIZ or ROX as the size standard.

  • Oligo synthesis ( Material production service )

  • Resequencing of PCR amplicons ( Material analysis service )

  • RFLP genotyping service ( Material analysis service )

  • RNA synthesis service ( Material analysis service )

  • SNP genotyping service ( Material analysis service )

  • SSLP genotyping service ( Material analysis service )

  • Whole genome assembly DNA sequencing service ( Material analysis service )

Software

  • 4Peaks ( Software )

    This software is used to edit and plot numerical datasets.

  • ABI 3130X Data Collection v.3.0 ( Software )

    This software collects and analyzes data from the ABI 3130X Genetic Analyzer.

  • 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."

  • Consed ( Software )

    "Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information."

  • Enzyme X ( Software )

    Software features: "Restriction enzyme information for over 580 commercially available enzymes; fully featured DNA sequence editor; directly search and download sequences from the NCBI Entrez nucleotide database; determine which buffer is most suitable for a double digestion; numerous helpful tools and calculators, and includes handy reference data like codon tables and amino acid tables."

  • 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."

  • Oligo ( Software )

    Primer analysis software for "designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis."

  • Phrap ( Software )

    "A program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets."

  • Phred ( Software )

    "Software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base."

  • Polyphred ( Software )

    "A program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions."

  • Primer3 ( Software )

    "Pick primers from a DNA sequence."

  • Sequence Scanner ( Software )


Web Links:

Last updated: 2012-07-16T15:27:15.554-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016