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Gene Expression & Genotyping

Services

The Gene Expression & Genotyping Facility (GEGF) facilitates implementation of high throughput genetic technologies for the research conducted by members of the Case community.

Primary Services

Gene Expression (Affymetrix)

  • Help with selection of the appropriate technology & technology format to meet experimental needs
  • Brokerage of microarrays (3’-expression array, Whole Transcript Arrays & the Transcriptome Arrays)
  • Preparation of sample for interrogation on microarray
  • Processing user-prepared and/or facility-prepared RNA on expression microarrays
  • Experience with a variety of labeling protocols to accommodate standard and small quantities of RNA (ng), as well as RNA isolated from Formalyn-Fixed Paraffin Embedded material
  • Assess Data Quality. Data reduction/data analysis
  • Low cost access to valuable, advanced, server-based data mining and annotation tools

Gene Expression (RT PCR)

  • Brokerage of ABI RealTime PCR assay kits and reagents
  • Preparation of archive cDNA from RNA
  • RT PCR assay set-up for relative quantitation and absolute quantitation
  • Help with selection of appropriate endogenous controls for RT Studies
  • Help with data interpretation/analysis
  • Endogenous control determinations

SNP Analysis (Affymetrix)

  • Help with selection of the appropriate technology & technology format to meet experimental needs
  • Brokerage of Affymetrix genotyping Arrays (6.0, CytoScan or a choice of arrays using the Axiom chemistry)
  • Sample preparation
  • Processing of sample on Affymetrix Array
  • Assess Data Qualityi

SNP Analysis (ABI)

  • Help with selection of the appropriate technology & technology format to meet experimental needs
  • Sample prep (open array or 384 well format, high throughput enabled by Matrix robotics)
  • Endpoint plate reading (high throughput enabled by ABI autoloader)
  • Measurement of real time spectral data (initial validation) on 7900
  • Basic PCR execution on 9700
  • Matrix robotics (programmable for custom set-up)
  • Help with analysis

Library Preparation & Capture for Next Generation Sequencing

  • Help with selection of the appropriate technology & technology format to meet experimental needs
  • Experience with both Custom and Exon Capture Protocols
  • Experience working with DNA isolated from blood, saliva, solid tissue and from Formalyn Fixed-Paraffin-Embedded material
  • Experience working with a variety of protocols, including Illumina TruSeq, Illumina TruSeq Amplicon Protocol, Agilent SureSelect Protocols, Qiagen GeneRead Sequencing Panels, etc.
  • Developed High Throughput Protocols to process 48 samples in a group

Nucleic Acid Isolation, Quality Assessment and Quantitation

  • RNA and DNA are isolated from FFPE Material
  • Accurate quantitation of Nucleic Acid samples is achieved using Qubit or a Nanodrop spectrophotometer
  • Quality assessment performed using the BioRad Experion or the Agilent TapeStation
  • Quality also assessed using RealTime PCR based assays such as quantifilier or PCR to amplify amplicons of varying sizes

Additional Services

  • Individually tailored consultation with potential users
  • Assistance with grant preparation
  • Assistance with experimental design
  • Serve as resource for linking users to databases, expression array data, etc.
  • Provide 3 credit hour course on issues pertaining to high throughput genomics technologies
  • Regular software workshops/training

Fees

Visit http://www.gegf.net to obtain fees for Arrays and Services.

Remember to acknowledge the valuable services provided by Cancer Center Core Facilities in your research papers and publications: 
"This research was supported by the Gene Expression & Genotyping Core Facility of the Case Comprehensive Cancer Center (P30CA043703)."

Contact for Information

Location: Wolstein Research Building, 3-401

Director: Martina L. Veigl, PhD
216.368.5689
mlv2@case.edu

Manager: Debora Poruban
216.368.8748
dcp10@case.edu

Director

Martina L. Veigl, PhD
Associate Professor, General Medical Sciences (Oncology)
mlv2@case.edu 

Gene Expression + Genotyping Core Facility Home Page

More information available on the Gene Expression + Genotyping Facility home page.