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

Sequencing Platforms

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

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)

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

Nucleic Acid Quantitation/Quality Check/Sizing Platforms

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

BluePippin

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

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

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

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

RNA Expression Analysis Platform

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)