Sequencing and Genomic Technologies

sequencing-and-genomic-technologiesGenomic technologies are among the most important experimental tools in modern research. Their importance will unquestionably grow in the coming years as declining prices allow for ever-larger projects, powerful new instrumentation provides increasingly precise data, and entirely novel applications appear.

Duke’s Sequencing and Genomic Technologies Shared Resource was created by the recent merger of two existing Duke Center for Genomic and Computational Biology units, the Microarray Core Shared Resource and the Genome Sequencing Shared Resource. Each of these predecessor cores has a track record more than a decade long of providing constantly updated, state-of-the-art genomic services. Access to the new Sequencing and Genomic Technologies Shared Resource offers all of our partners the full range of genomic technologies, making it much simpler for researchers to find the right service for their needs. The size and scope of this resources provides our partners with access to comprehensive consultation, seamless management of complex projects that span multiple services, enhanced operational flexibility, and economies of scale for support services. Genomic tools that are provided through partnership include the following:

Variant Detection:

  • Targeted variant discovery
  • Exome sequencing
  • Whole genome sequencing
  • RAD-Seq
  • De Novo Sequencing
  • Mate-pair
  • Pacbio sequencing
  • DNA-Seq
  • Whole transcriptome

Functional Genomic Assays:

  • ChIP-seq
  • RNA-seq
  • small RNA-seq
  • Ultra-Low-Input RNA-seq
  • Targeted RNA-seq
  • RNA-seq for FFPE
  • DNA modification sequencing
  • FFPE gene expression assays
  • Single cell gene expression assays
  • miRNA assays through RT-PCR assays and microarrays
  • RT-PCR and Fluidigm Biomark
  • HDMicrobiome Analysis

Proteomics and Metabolomics

metabalomics

The School of Medicine, the Duke Center for Genomic and Computational Biology, and the Duke Cancer Institute all collaboratively work with the Proteomics and Metabolomics Shared Resource to provide protein characterization resources for the Duke Research Community and our partners. These services include protein identification and protein quantitation from a wide variety of sample types from simple mixtures (gel spots and bands) to complex mixtures (protein complexes, cell lysates, and plasma).

The Proteomics and Metabolomics Shared Resource uses mass spectrometry as the key technology for the qualitative and quantitative characterization of proteins. Protein identifications are made using state-of-the-art database search engines running on a dedicated high speed Blade cluster, with the capability of searching standard or custom protein databases. The proteomic capabilities currently offered include:

    • Open (unbiased) qualitative and quantitative analyses using high resolution, accurate mass data for high confidence identifications and good quantitative reproducibility, preferred tool for differential protein expression and biomarker discovery, performed on hybrid quadrupole/time-of-flight tandem mass spectrometers coupled with ultra-performance nanoscale capillary liquid chromatographs (LC/ESI/MS/MS)
    • Targeted protein quantitation for high sensitivity, high specificity and excellent quantitative reproducibility, preferred tool for protein expression verification -performed using LC/ESI/MS/MS with multiple reaction monitoring (MRM) on a triple quadropole tandem mass spectrometer
    • Characterization of post-translational modifications, including phosphorylation
    • Multidimensional characterization of gas-phase structures of peptides, intact proteins and protein complexes based on mass, size, shape, and charge – performed on a hybrid quadrupole/traveling wave ion-mobility/time-of-flight tandem mass spectrometer (LC/ESI/MS/IMS/MS)

For more information about the Duke Sequencing and Genomic Technology core click here.