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Genomic Analysis

Genomic Analysis

A variety of facilities at Penn State College of Medicine help internal and external investigators with genomic analysis, including the Genome Sciences Facility, the Zebrafish Functional Genomics Core and the Macromolecular Synthesis Core Facility.

Genome Sciences Facility

The full-service Penn State College of Medicine Genome Sciences Facility provides consultation, instrumentation and services to both Penn State and non-Penn State investigators in genomic, epigenomic and transcriptomic studies.

The variety of instrumentation allows for capabilities ranging from highly focused analysis of candidate SNPs and mRNAs to whole genome, exome, epigenome and transcriptome sequencing. Services are also available for a variety of study designs extending from a few laboratory samples to large clinical projects involving hundreds or thousands of samples. The full bioinformatics service is also available for data analysis.

About the Genome Sciences Facility

The facility resides in 5,000 square feet of newly renovated space, encompassing separate "pre-amplification" and "post-amplification" rooms to prevent any contamination of PCR-amplified materials to pre-processed input DNA/RNA samples. Four well-experienced staff members are available for assisting in project operations. In addition, the lab space is available for investigators who need temporary room for sample preparation.

We receive either tissue, DNA/RNA, or customer-generated NGS libraries. We process samples accordingly based on agreement reached during consultations on the design of the experiment. We develop new applications to accommodate state-of-the-art NGS technologies. We conduct sequence read alignment, secondary analysis (quantitation, variant calling, functional annotation, visualization, etc) and follow-up with the interpretation of the results. We provide support for grant writing and hands-on training for students and post-docs in NGS processing.


A variety of instrumentation is available in the Genome Sciences Facility for sample processing, sample quantitation and quality control, qPCR/digital PCR, microarray analyses, next-generation sequencing and other needs.

Sample Processing

Sample Quantitation and Quality Control

qPCR/Digital PCR

Microarray Analyses

Next-Generation Sequencing (NGS)


  • Illumina GenomeStudio
  • Illumina iCompute
  • Ingenuity Pathway Analysis

For Ingenuity Pathway Analysis access information, please contact the IS Service Desk at 1-833-577-HELP (4357) or

Additionally the facility contains refrigerators, -20ºC and -80ºC freezers, and associated small equipment (e.g. multichannel, electronic, and accordion pipettes, centrifuges, etc.).

Contact Us

For details on the Genome Sciences Facility, email or call 717-531-5823.

Zebrafish Functional Genomics Core

The Zebrafish Functional Genomics Core at Penn State College of Medicine was established to provide the Penn State research community with a modern, centralized facility for housing, breeding and performing experiments with zebrafish, one of the fastest growing model systems in biomedical research, as well as the intellectual infrastructure to do that work.

About the Facility

The Zebrafish Functional Genomics Core is a newly designed facility housing a state-of-the-art Pentair Aquatic Habitats recirculating aquaria, housed in the Department of Comparative Medicine.

The central housing room is equipped with 32 racks of recirculating aquaria, able to accommodate any combination of 1, 3 and 10 liter tanks.

Other facilities include twin 16-rack recirculating systems with independent filtration/purification, an isolated quarantine room with three stand-alone housing systems, a sentinel pathogen-monitoring program, a procedure room and three independently controlled light-tight breeding cabinets.

See photos of the facility taken during its April 2016 grand opening.

This image of the Zebrafish Functional Genomics Core at Penn State College of Medicine, taken during its April 2016 grand opening, shows an aisle framed by five shelves of zebrafish tanks down either side. The tanks appear deep blue, and zebrafish can faintly be seen swimming in the frontmost ones.
Penn State College of Medicine's Zebrafish Functional Genomics Core opened in April 2016.


The Zebrafish Functional Genomics Core provides a variety of instrumentation for microinjection and fluorescence imaging.


  • Eppendorf FemtoJet microinjectors
  • Manual micromanipulators
  • ZEISS Stereo Discovery.V8 microscopes

Fluorescence Imaging

  • Leica MZ FLIII Fluorescence Stereomicroscope
  • Olympus MVX10 MacroView Macro Zoom Fluorescence Microscope
  • ZEISS Axio Zoom.V16 Zoom Fluorescence Microscope with ZEISS ApoTome.2


Fish are available to both Penn State College of Medicine and external investigators. We currently house the following wild type lines: AB, Conner, Ekkwill, Liles, Tübingen (Tu) and WIK. We also house a selection of mutant and transgenic lines.

Contact Us

For details on the Zebrafish Functional Genomics Core, email Khai Chung Ang, PhD, Scientific Director, at or call 717-531-4704.

Macromolecular Synthesis Core

The Macromolecular Synthesis Core Facility was established in 1987-88, with primary grant support from the National Science Foundation as well as College of Medicine funds. This facility subsequently received grant support from the NIH and the State of Pennsylvania via the Ben Franklin Partnership, and matching funds from the College of Medicine.

About the Facility

The Macromolecular Synthesis Core Facility is heavily used, and generates approximately 2,000 oligonucleotides and 100 peptides per year to investigators around the US. Funding from NIH, NSF, Pennsylvania Department of Health Tobacco Settlement Funds (CURE) and State of Pennsylvania grants have helped to provide instrumentation for these services.


  • Peptide Synthesis
  • Oligonucleotide Synthesis

Contact Us

For details on the Macromolecular Synthesis Core, email Anne Stanley, Lab Manager and Senior Research Support Associate, at or call 717-531-6087.

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