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.
Instrumentation
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
- QIA Symphony DNA/RNA Extraction Robot
- Bullet Blender (high-throughput tissue homogenizer)
- Covaris Adaptive Focused Acoustics Ultrasonicator E-Series
Sample Quantitation and Quality Control
- Agilent 2100 Bioanalyzer
- Nanodrop ND-1000 Spectrophotometer
- Qubit Fluorometer
- Molecular Devices UV/Vis/Fluor Spectrophotometer (available in Drug Discovery Core)
qPCR/Digital PCR
- ABI QuantStudio 12K Flex system with available OpenArray block
- ABI QuantStudio 3D Digital PCR System
Microarray Analyses
Next-Generation Sequencing (NGS)
Other DNA Sequencing
- ABI 3130XL Capillary Sequencer (Sanger sequencer and associated genotyping or DNA fingerprinting applications)
Software
- Agilent Genespring
- Illumina GenomeStudio
- Illumina iCompute
- Ingenuity Pathway Analysis
Agilent Genespring and Ingenuity Pathway Analysis access information is available through the Bioinformatics Core.
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 genomesciences@pennstatehealth.psu.edu 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.
Instrumentation
The Zebrafish Functional Genomics Core provides a variety of instrumentation for microinjection and fluorescence imaging.
Microinjection
- 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
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 kca2@psu.edu 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.
Facility Details
The Macromolecular Synthesis Core Facility is heavily used, and generates approximately 2,000 oligonucleotides, 100 peptides and 40 protein sequences per year. A wide range of faculty from the College of Medicine use this core lab, as do many outside contractors. The goal has been to offer fair market costs, with the charges for services used to offset chemical and maintenance costs. Funding from NIH, NSF, Tobacco Settlement Funds and State of Pennsylvania grants have helped to provide instrumentation for important new research services.
Services
- Protein Sequencing
- Peptide Synthesis
- Oligonucleotide Synthesis
- Image analysis and Gel Band Quantitation (Instrumentation purchased with Tobacco Settlement Funds)
Contact Us
For details on the Macromolecular Synthesis Core, email Anne Stanley, Lab Manager and Senior Research Support Associate, at astanley@psu.edu or call 717-531-6087.