Facility details and available services

Genome Sciences Core Facility




Facility Details: (TO BE UPDATED)

Nucleic acid processing and analysis: The Facility maintains equipment for nucleic acid extraction (QIAsymphony and Bullet Blender), sonication (Covaris adaptive focused acoustics ultrasonicator E-series), quantitation and quality control (Agilent 2100 Bioanalyzer, Nanodrop Spectrophotometer, Qubit, and access to a Molecular Devices FlexStation 3 UV/Vis/Fluor spectrophotometer). An LifeTech QuantStudio 12K Flex system with robotic plate handler and QuantStudio 3D digital PCR system is available for qPCR gene expression and genotyping services. The Facility provides custom Sanger sequencing of plasmid, PCR and BAC templates. We can also run fragment analysis assays including footprinting, microsatellite, loss of heterozygosity (LOH), SSCP, RFLP and genotyping/SNPlex (multiplexed SNP analysis). Cost for each service is as follows (we allow walk-up and free usage of Nanodrop and Qubit, please inquire for the usage of FlexStation 3) :


Microarray: The Facility offers Illumina platforms as the main microarray-based procedure for genotyping and gene expression. The recently acquired iScan system allows high-throughput and cost-effective microarray analysis of genotyping, gene expression, copy number analysis, methylation analysis and LOH studies. Roche and Agilent microarray equipment is also available. Individual SNP calls can be confirmed by PCR tools described above. Listed below are the costs of some popular microarrays.

Next Generation Sequencing platforms:
For next generation sequencing projects the Facility offers a range of workflows depending on investigator needs and number of reads/length of sequence required for the project. The Facility contains a MiSeq system to perform low output applications (from 300 Mb to 7.5 Gb in ~4 to 39 hours) and a HiSeq 2500 system, which allows data collection in both rapid run (up to 90 Gb/flow cell, 2×150 bp, in 40 hours) and high output modes (up to 300 Gb/flow cell, 2×100 bp, in ~11 days) on either one or two flow cells. The Facility also maintains a LifeTech Ion Proton DNA sequencer for targeted sequencing and exome sequencing (10 Gb with sequencing run time of 2-4 hours). An Apollo 324 robotic system supports a variety of automated library preparation protocols for whole genome, whole exome, ChIP-seq, RNA-seq and targeted resequencing. Listed below are currently operated services, but we are expanding the service to meet the needs of each investigator.


Bioinformatics Support: The Penn State College of Medicine has three dedicated High Performance Computing (HPC) systems with a total of 136 CPU Cores, 768GB RAM and 50TB of local storage in addition to the 80 TB Storage Area Network (SAN). For the non-human subject samples, we also have access to the world class High Performance Compute systems at Penn State University Park, including BioSTAR (512 processor cores, 4 TB of aggregate memory, and 624 TB of disk storage) and CyberSTAR (1,920 cores and 7.68 TB memory, and 650 TB storage). We conduct sequencing reads alignment, secondary analysis (quantitation, variant calling, functional annotation, visualization, etc), as well as statistical analysis correlating genomic with phenotypic information. There is no charge for the consultation and we encourage each investigator to make an appointment with Director/staff in advance to secure enough time for discussion. Director’s availability is found in the 5th tab of below web site(http://sites.psu.edu/yuka/). Bioinfomatics service will be charged at $50 per hands on hour. Each project is different, so investigators are encouraged to contact us to estimate the necessary hours for each project.