©2009 UTMB Molecular Genomics Core (MGC)

ABOUT AFFYMETRIX GENECHIPS
Service Information
GeneChip Technology
GeneChip FAQ
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Available GeneChips

The Molecular Genomics Core (MGC) has processed thousands of GeneChips for UTMB investigators since its inception in 2000. Because of the complexity and expense of these projects, the MGC staff offers a more collaborative effort for experimental design and data analysis.  GeneChip hybridization technology makes it possible to assess the relative mRNA expression level of tens of thousands of genes in a single experiment.  Samples should be submitted in the form of total RNA either frozen or as an ethanol precipitate.  Once received, sample quantity will be determined via the NanoDrop which will be used to normalize the samples for the labeling reaction.  Two hundred nanograms of sample will then be used to assess the integrity of the sample via the Agilent BioAnalyzer.  Once samples pass QC, expression analysis will be carried out on our Affymetrix GeneChip system and a detailed report generated. Each report consists of sample concentration, sample quality (Electropherogram and Gel-like image), GeneChip quality report, and a list of candidate genes with relative ratios and associated p-values.
Due to the large volume of data generated by these types of experiments, specially written software programs are needed to manage and analyze the data. The MGC employs Partek Genomics Suite for secondary analysis and Ingenuity Pathway Analysis  for canonical pathway identification.  Once gene expression analysis is complete, we are further able to assist with the validation of this data by performing real-time PCR for a quantitative measurement of transcript levels. The combination of microarray data and Real-Time qPCR validation provides researchers with a strong list of candidate genes for further evaluation in their particular system.

Affymetrix Genechip Services

  • GENE EXPRESSION - 3´Expression Arrays interrogate each gene with multiple independent probes, offering the most accurate, robust and reproducible 3´-based, gene-level expression profiling on a genome-wide scale with the industry-standard platform.
  • SNP GENOTYPING & CNV ANALYSIS - Power your association study with larger sample sizes in your initial whole-genome scan and statistical replication by using the Affymetrix Genome-Wide Human SNP Array 6.0—a single array that features more than 1.8 million markers for genetic variation, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 additional probes for the detection of copy number variation.

Service Features & Options

  • Experimental Design
  • Sample Quantitation via NanoDrop® ND-1000
  • Qualitative Sample analysis via Agilent BioAnalyzer®
  • Low Input (100ng)/High Input (5μg) Labeling Options
  • Data Analysis

Useful Links


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