Yuka Imamura Kawasawa

yimamura@pennstatehealth.psu.edu

Facility details and available services

Penn State College of Medicine Genome Sciences and Bioinformatics Core Facility

The Core is a full service facility and provides consultation, instrumentation, and analysis services to both Penn State and non-Penn State investigators in various comics studies. Four dedicated, well-trained staff members are available for executing all of the fee-for-service projects.

(http://med.psu.edu/core/genomics, http://med.psu.edu/core/informatics)

Facility Details: (UPDATED AS OF Jan2017)

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 Agilent TapeStation and a Molecular Devices FlexStation 3 UV/Vis/Fluor spectrophotometer). A LifeTech QuantStudio 12K Flex system with robotic plate handler and QuantStudio 3D digital PCR system is available for qPCR gene expression and genotyping applications. The Facility also provides custom Sanger sequencing by an ABI 3130XL. We have recently acquired Fluidigm’s C1 Single-Cell Auto Prep System which allows accurate and cost-effective isolation of single cells and downstream DNA/RNA extraction including cDNA synthesis; all can be conducted within a single chip.

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.

Next Generation Sequencing platforms: 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 Illumina’s MiSeq, a HiSeq 2500 system, and most recently, NovaSeq 6000 system was installed, as well as a LifeTech Ion Proton DNA sequencer. A BioNano Irys and Saphyr have been recently added, that can be used for whole genome mapping and identifying larger structural variations such as indels or copy number variations. 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

Bioinformatics: The Facility is equipped with a dedicated high performance computing environment with a total of 1 Petabyte of enterprise storage. Total RAM of the system is 4864 GBs with the standard and high memory compute nodes providing 10.5 GBs of RAM and 24 GBs of RAM per core respectively. The Penn State College of Medicine Research Informatics group (http://med.psu.edu/core/informatics) is available for full support of the operation and maintenance of the HPC system. Various software packages and necessary genomic references are in place and being routinely updated to meet the needs in fast-developing bioinformatics applications.

Bioinfomatics service will be charged at $50 per hands on hour for internal investigators ($60 for external non-profit/academic). Each project is different, so investigators are encouraged to contact us to estimate the necessary hours for each project. Below are representative analysis services we provide.

  • DNA Next Generation Sequencing (NGS) analysis
  • Exome-Sequencing analysis (whole exome, targeted gene panel)
  • ChIP-Seq analysis (narrow peaks or wider domains)
  • RNA-Seq analysis (mRNA, small (micro) RNA, single cell, FFPE or degraded RNA, any species including yeast, virus, bacteria etc)
  • DNA Methylation Sequencing analysis (whole genome, RRBS (reduced representation of bisulfite sequencing), targeted)
  • Metagenome analysis (16S rRNA-seq, shotgun metagenome (whole genome))
  • Ribo-Seq analysis
  • Differential Expression (RNA-Seq, microarray, DNA methylation)
  • Variant Discovery (DNA & RNA-Seq, microarray)
  • Junction-based analysis of splicing events
  • ENCODE correlations with NGS datasets
  • The Cancer Genome Atlas (TCGA) NGS datasets
  • Epigenetic Signature discovery
  • Transcription Factor Motif discovery
  • Phosphorylation prediction
  • microRNA Target prediction
  • De novo Assembly
  • Microarray analysis
  • Time-series Microarray analysis
  • Biomarker panel design
  • Pathway analysis
  • Gene Ontology analysis
  • Proteomics analysis
  • qPCR analysis
  • Machine Learning
  • Custom scripts/software

 

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