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 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
Pacific Biosciences Sequel System IIe (PacBio)
Based on the proven performance of the Sequel II system, the Sequel IIe system delivers:
- Direct access to the only highly accurate long reads: PacBio HiFi reads
- Deeper biological insights, less data processing, and faster results thanks to the unmatched clarity of HiFi reads
- Reliable and affordable high-throughput sequencing for a broad range of applications
- 8 million ZMWs per SMRTcell
Key benefits of HiFi sequencing on the Sequel IIe system:
- Better data for superior results with lower coverage, from a single technology
- Less time spent on data processing and analysis for faster answers
- Cost savings at every step of your sequencing pipeline
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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
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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)
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