Genomic Analysis

Genomic Analysis

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Genomic Analysis

Core Facilities Genomic Analysis Basic Content

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.


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Core Facilities Genomic Analysis Genome Sciences Facility Tab Code

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.