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Genomics Core Facility

The Genomics Core Facility, located on the 17th floor of the New College Building, 245 N. 15th Street in Philadelphia, is home to a variety of instrumentation platforms available to assist researchers across Drexel University with gene (DNA and RNA) sequencing and nucleic acid quantitation.

Available Platforms

DNA/RNA Sequencers

Sequence-Specific Nucleic Acid Quantitation/Quality Check/Sizing

RNA Expression Analysis


Sequencing Platforms

Illumina NextSeq Midi

Illumina NextSeq 500

  • Bench top: slots in between MiSeq and HiSeq
  • 120 gigabases of sequence; 40x coverage of human genome/run
  • Expected upgrades over next year or so should take in to 3 human genomes/run
  • 12 and 30 hour cycle times
  • Short reads: 1x75 bases; 2x75 bases; 2x150 bases
  • Has two flow cell configurations – mid (132M clusters) and high (400M clusters)
    • 1-16 exomes/run
    • 1-20 transcriptomes/run
    • 6-96 targeted panels/run
    • 12-40 gene expression profiling samples/run

Drexel's Genomics Core Facility instrument: Illumina MiSeq

Illumina MiSeq

  • Up to 15 gigabases of output
  • Read Length: 1x36 bp, 2x25 bp, 2x75 bp, 2x150 bp, 2x250 bp, 2x300 bp
  • ~4 to ~56 hour run time
  • 4 M to 44-50 M clusters

Pacific Biosciences Sequel System (PacBio)

Pacific Biosciences Sequel System (PacBio)

  • 1 million ZMWs per SMRTcell
  • Longest average read lengths
  • Highest consensus accuracy
  • Uniform coverage
  • Simultaneous epigenetic characterization
  • Single-molecule resolution

 
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Nucleic Acid Quantitation/Quality Check/Sizing Platforms

Bio-Rad QX-200 Droplet Digital PCR

Bio-Rad QX-200 Droplet Digital PCR

  • Absolute quantitative limiting dilution PCR for DNA or RNA – based on Poisson distribution
  • Analogous to 454 emulsion technology – partitions ddPCR mix into 20K nL droplets (one template max/droplet)
  • EvaGreen or Taqman-type hydrolysis probe-based
    • Droplet digital PCR instruments
      • C1000 touch thermal cycler – performed on partitioned droplets
      • PX1 plate sealer
    • Droplet generator
    • Droplet reader – droplets are sipped and run single file past a two-color detector
      • # of positive and negative droplets is counted to give discrete quantitative data
  • No need for standard curves
    • NGS library quantitation for multiplex strategies
    • Gene expression studies
    • Copy number variations
    • Viral load
    • Cancer biomarkers

Drexel's Genomics Core Facility instrument: BluePippin

BluePippin

  • DNA size selection for next-gen sequencing, with pulsed field
  • 100bp – 50kb
  • Collect HMW DNA with high-pass filtering

Drexel's Genomics Core Facility instrument: Femto Pulse System

Femto Pulse System

  • Large fragment resolution – separate high molecular weight DNA smears and fragments through 165 kb
  • Achieves 10 times higher sensitivity for nucleic acid smears and up to 100 times higher for nucleic acid fragments
  • Detects nucleic acids down to 50 fg/µL input concentration, making the Femto Pulse System ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low-concentration samples

Drexel's Genomics Core Facility instrument: 2100 Bioanalyzer Instrument

2100 Bioanalyzer Instrument

  • Objective assessment of sizing, quantitation, integrity and purity from DNA, RNA and proteins
  • Minimal sample volumes are required for an accurate result

Drexel's Genomics Core Facility instrument: Qubit 4 Fluorometer

Qubit 4 Fluorometer

  • Latest version of the popular Qubit fluorometer
  • Accurately measure DNA, RNA and protein quantity
  • RNA integrity and quality
  • High levels of accuracy using only 1–20 μL of sample

 
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RNA Expression Analysis Platform

nanoString

nanoString

  • nCounter analysis system – for targeted quantitative nucleic acid analyses
  • Highly multiplexable – can look at up to 800 targets simultaneously
    • Digital – no amplification, uses nanotech colored barcodes
      • Each target unique bar code
    • Sensitive – more sensitive than PCR-based systems
    • DNA (CNV), mRNA, miRNA, lncRNA, ChIP-string analysis
    • Very small sample sizes
      • In vivo studies of pathogen gene expression
      • Single cell expression
  • Workflow
    • Set up hybridization between target and nCounter probes
    • Hybridize and wash ON on robotic prep station
    • Move hybridization cartridge to digital analyzer
    • Unparalleled sensitivity (< 1 copy/cell), reproducibility (R2 > .99), and dynamic range (5 logs)

 
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