Genomics & Protein Lysate Array

The Genomics Core is dedicated to the successful use of genomic analysis by Cancer Center members. Our goal is timely, state-of-the-art service, training, or advice to members on the use of genomic analysis, with an emphasis on data quality and value to the investigator.

Services

Gene Expression Analysis

The Genomics Core offers the Illumina, Affymetrix, NimbleGen, and Agilent platforms for gene expression analysis. The predominant array layouts are whole genome arrays for both human and mouse; however, other formats such as rat and zebrafish are also available. Each platform offers unique advantages, which can be explained by the Genomics Core Director. The cost varies by array type and vendor.

Quantitative RT PCR

QRTPCR provides an investigator the opportunity to interrogate more modest numbers of genes with higher quantitative accuracy than with array analysis. It is often used to confirm array results. New QRTPCR platforms allow interrogation of expression in 96- or 384-well formats with the potential for multiplexing by using a variety of fluorescence-tagged markers. The Genomics Core offers QRTPCR analysis in 96-well plate format using either dye intercalation (Syber Green) or tagged primer sets (Taqman).

SNP Genotyping/Copy Number Analysis

This resource offers Array-based Comparative Genomic Hybridization (aCGH) that uses the Illumina HumanOmni1-Quad Whole-Genome array, and NimbleGen Mouse CGX (3x720K) array.

Illumina's Omni platform offers researchers the flexibility to genotype samples with hundreds of thousands to millions of markers that deliver dense genome-wide coverage with the most up-to-date content available from the scientific community. SNP markers are strategically selected to provide maximum coverage of the genome for both association testing and copy number detection. By analyzing signal intensity at each SNP location, DNA copy number can be estimated, thereby providing an investigator with data on the copy number of genes on their samples. This methodology is rapidly replacing BAC arrays for copy number analysis.

NimbleGen offers cost-effective array analysis of three samples on a single slide. The cytogenetics (CGX) design is for genome-wide analysis of DNA copy number changes with a subset of probes focused in disease-associated regions. NimbleGen also offers several other types of CGH/CNV arrays for a variety of organisms to meet your specific research needs.

MicroRNA Expression

This resource offers the Exioqn miRCURY LNA™ microRNA Array system for global microRNA expression profiling. Users can choose to perform either single-color or two-color experiments. The system is based on the LNA™-technology, which offers unique advantages in the specific and sensitive detection of short RNA sequences. One type of array contains more than 1,891 capture probes, covering all human, mouse, and rat microRNAs; the other contains close to 2,500 capture probes from 85 species other than human, mouse, and rat.

Quantum Dot Based Reverse Phase Protein Array (Qdot-RPPA)

This service provides quantitative protein functional analysis. It can be applied to the proteomic profiling and biomarker identification using cell lines or clinical samples, the proteomic response patterns using siRNA/miRNA libraries, and the protein kinetic responses in time scale and dose gradient. The major advantages of Qdot-RPPA compared to the traditional Western blots are large sample throughput (up to 160 samples/array), less sample consumption, 1,000-fold more sensitive, and much broader linear dynamic range for quantification.

Bioinformatics Support

To help users to analyze their data and get meaningful information, the Genomics Core provides a computer workstation with several state-of-the art commercial bioinformatics software programs:

  • Nexus (BioDiscovery, Inc.) is an integrated software suite for copy number discovery, gene expression, and methylation analyses. It also helps users to visualize their data, link the data to external bioinformatics databases, and generate figures for publication.
  • Partek Genomics Suite (Partek, Inc.) provides integrated software for gene and miRNA analysis, copy number, and single nucleotide polymorphism analysis. It provides not only powerful statistic tools for statistical analyses, but also graphic tools for publications. This suite is for the sophisticated user.
  • Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Inc.) helps users integrate array data with biological context. It not only provides insight into the molecular and chemical interactions, cellular phenotypes, and disease processes based on the Ingenuity Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships, but also facilitates informed decision-making, advance research project design, and generates new testable hypotheses.

Users can either come to the Genomics Core to use the software or purchase a floating license for access at their own computer. The Genomics Core also provides routine bioinformatics support to help users analyze their array data and generate figures. The service fee is $90/hour.

For large high throughput projects, the Genomics Core will facilitate the analyses between users and the Bioinformatics Shared Resource.

Fees

The price for Gene Expression arrays includes a total RNA quality check before labeling and after cRNA synthesis, data quality check after scanning, and Excel or other format spreadsheet with gene fold-change or other user identified values.  

Genomic ServicesCost per Sample
Illumina Human HT12v4 Expression Array $240/sample (12 samples/array)
Illumina Mouse 6v2 Expression Array $315/sample (6 samples/array)
Illumina Human Omni2.5-8v1 Array $600/sample (8 samples/array)
Illumina 450K Methylation Array $495/sample (12 samples/array)
Illumina Human DASL Array for FFPE samples $275/sample (12 samples/array
Affymetrix Human Genome U133 Plus 2.0 Array $735/sample (1 sample/array)
Affymetrix Mouse Genome 430 2.0 Array $735/sample (1 sample/array)
Affymetrix Zebrafish Array $561/sample (1 sample/array)
Affymetrix Drosophila Array $585/sample (1 sample
NimbleGen CGX (3x720K) Array $600/sample (3 samples/array)
NimbleGen Methylation (3x720K) Arra $630/sample (3 samples/array)
Exiqon miRNA 6th Generation Array $500 (1-color), $600 (2-color)/sample
Exiqon miRNA 7th Generation Array $515 (1-color), $615 
Experion RNA Quality Check $60 up to 12 samples
TaqMan SNP Genotyping/qPCR $.95 per well plus $10 plate cost
Total RNA Preparation using Qiagen Plus Kit $50/sample