Genomics Facility

The Genomics Facility is managed by our Professor of Practice, Jutta Marzillier, Ph.D. If you would like further information about the facility and how it might enhance your research, please contact Dr. Marzillier at 610-758-4902.

User fees apply for instrumentation use and technical support. Departmental Liaison memberships as available, which includes a reduced fee schedule. Please contact Maria Brace, Department Coordinator, for more information.

With the onset of the “post-genomic era” approximately ten years ago, the demand for high-throughput screening is rapidly growing, thus advancing the microarray technology extensively used in biological research. This technique uses parallel hybridization of thousands of gene sequences to measure levels of gene expression in RNA samples and make comparisons between samples.

The Genomics Core Facility contains the following equipment and resources:

Applied Biosystems 7300 Real-Time PCR System

The 7300 system supports many real-time quantitative PCR application needs. 

• Gene expression analysis (relative and absolute quantitation)
• Allelic discrimination (SNP genotyping assays)
• Plus/minus assays
• 96-well plate or 8-strip 0.2 ml tube format
• Single excitation with emission filters optimized for use with FAM™/SYBR® Green I, VIC®/JOE™, NED™, TAMRA™, and ROX™ fluorescent dyes.
• Use with SYBR® Green or TaqMan® Universal PCR master mixes
• Sequence Detection Software SDS v1.4 to analyze data
• Primer Express 2.0 software for designing primers (ABI)
• Quantitative PCR run time less than two hours
• Electronic delivery of qRT-PCR data

Applied Biosystems 310 Genetic Analyzer

The ABI 310 capillary sequencer offers reliable sequencing for a small number of cloning and PCR products using Sanger chemistry. 

• Cycle sequencing reaction using BigDye® Terminator reagent, v3.1
• Reading length approximately 800 base pairs
• DNA sequencing analysis software, v5.1
• Electronic delivery of sequence data

RNA Isolation

Isolation of high quality RNA suitable for quantitative Real-Time PCR or microarray analysis

• RNA isolation using Trizol or RNeasy method
• Additional DNase digest performed upon request
• Spectrophotometric QC using Nanodrop
• Further RNA QC possible with Agilent 2100 Bioanalyzer (see below)

DNA/ RNA analysis and Quality control

DNA, RNA and labeled cRNA samples can be quickly evaluated on a NanoDrop ND-1000 and further assessed on an Agilent Bioanalyzer 2100. 

NanoDrop ND-1000

• Highly accurate, fast analysis of samples as small as 1 μl
• Full-spectrum UV-Vis absorbance analyses (220-750 nm)
• Large dynamic range: 1.5-3700 ng/μl of ds DNA, 1.5-3000 ng/μl of RNA
• No dilution for most samples
• No cuvettes or capillaries

Agilent Bioanalyzer 2100

• fast RNA analysis of samples as small as 1 ml
• assess total RNA quality by observing the 18S and 28S ribosomal peaks and their ratio, or the 16S and 23S peaks of prokaryotes
• use of RNA6000 Nano and Pico Series II Chips
• qualitative range: nano: 5-500 ng/ul total RNA in water; pico:  50-5000 pg/ul total RNA in water
• sample size: 1 ul

Gene expression analysis using the latest Agilent technology (hybridization onto 60mer oligonucleotides, 4x 44K features, 4 microarrays per slide)

• Amplification and labeling of target RNA into cRNA using Agilent Low RNA Input Linear Amplification Kit
• One-color or two-color gene expression assays
• cRNA fragmentation and Hybridization in rotating oven overnight with subsequent washing, stabilization, and drying
• Scanning in Agilent G2505B microarray scanner (scans all Agilent and non-Agilent microarrays with a 1”x3” slide format)
• fast scanning by simultaneous two color scanning at 5 or 10 micron resolution
• Automated extraction of Agilent microarrays
• Feature Extraction Software v9.1 with built-in error models
• Standard format data output including tab-delineated text and MAGE-ML files
• GeneSpring Data Analysis Software

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