GeneChip Analysis |
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The BRF performs gene expression analysis using the Affymetrix GeneChip system and synthetic oligonucleotide spotted array system (please see spotted arrays in BRF). The GeneChip system utilizes standard protocols for standard and small samples for synthesizing labeled cRNA starting with total RNA or mRNA, a hybridization oven for hybridizing the cRNA to the GeneChip, a fluidics station for washing and staining the chip, a laser GeneArray scanner for detecting fluorescence levels of all the probes on the chip (see pictures below), and a regiment of software for analyzing the resultant image and data, which will be described later in detail. Currently, Affymetrix provides chips for the following genomes: human (HgU133_Plus 2 is the most current chip with approximately 47,000 transcripts and variants, including 38,500 well-characterized human genes), mouse (Mouse Genome 430 2.0 Array is the most current chip, which contains approx. 45,000 probe sets for 39,000 transcripts and variants from over 34,000 well characterized mouse genes), rat (Rat Genome 230 2.0 Array is the most current chip which contains approx. 31,000 probe sets interrogating about 30,000 transcripts and variants from over 28,000 well substantiated rat genes) , Rat Toxicology U74 and Rat Neurobiology U74 with approx. 850 and 1,200 probe sets per chip respectively), Drosophila, yeast, E. coli , and Arabidopsis. The price for the chips ranges from $350 to $425, with the latter being the cost for the most current arrays. The processing cost for each sample is currently $375 which covers cRNA synthesis, chip hybridization and scanning, and preliminary data analysis and data mining. We also provide RNA isolation for an additional charge. Visit these links for more information regarding our quality control measures and data analysis methods. We strongly encourage our users to consult with us on the planning of their GeneChip experiments. We will gladly offer our advice in the experimental design, choice of chips, sample preparation, and coordination of experiment timings. You can contact us by e-mail or by phone: Yongde Bao (yb8d@virginia.edu, 982-2551) or Alyson Prorock (ajp7x@virginia.edu, 243-9689). For a first time user to officially place a GeneChip experiment order, please establish an account by going to the GEOSS website (http://genes.med.virginia.edu) developed under the collaboration with the GeneChip/Microarray Bioinformatics (GMB) Core, which also offers advanced statistical & Bioinformatics analysis services on microarray data. Then, click on the 'GEOSS Login' link. Follow the directions indicated in the GEOSS Instructions document or contact Jodi Kanter (ACHS, jlk3x@virginia.edu, 4-2846) at Academic Computing Health Sciences for technical assistance to initiate your account. For assistance in entering data, contact Alyson Prorock or Jodi Kanter. After your order has been placed, you will need to bring your samples to the MicroArray lab at the BRF (Jordan Hall, room 1051) or schedule a time for your samples to be collected or harvested (call Alyson Prorock). We accept tissue sections, cultured cells and isolated RNA as samples.
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