… to provide infrastructure for the
use of genomic technologies ...
• Microarrays
• High throughput genotyping

Services

• Affymetrix GeneChips®

We use Affymetrix GeneChips® for large-scale analysis of gene expression. Affymetrix also has GeneChips® for genome-wide SNP genotyping.

Obtaining good data requires careful consideration of experimental design and RNA preparation. Consultation with the Center at the earliest possible stage in experimental design is important. We have found that analyzing at least 4 to 6 biologically independent samples from each experimental condition allows powerful statistical analyses. We generally do not favor pooling; it is not a substitute for biologically independent samples. We can work with small amounts of RNA, using amplification procedures.

Analysis of these experiments can be complex, and should be planned when the experiment is planned. We can in some cases collaborate in analyses, or direct you to faculty who have experience in analyzing these data. Analysis is not included in our routine services.

• Please read the overview of Affymetrix Experiments before contacting the Center.

• All experiments must be discussed with Dr. Jeanette McClintick or Dr. Edenberg before submitting RNA samples to the Center for Medical Genomics. In considering sample size, a useful reference is McClintick, J.N. and H.J. Edenberg (2006) Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics 7: 49.

• Chunxiao Zhu and other CMG staff will consult with the investigator about RNA preparation.

We accept samples of total RNA. RNA quality must be high for good results; see Quality Control measures. Investigators should run a spectrum from 220 to 350 nm, and run samples on agarose gels to confirm that the ribosomal bands are intact, with the large band clearly darker, and with minimal DNA contamination. Concentration of samples should be above 1 microgram per microliter. We prefer to receive at least 6 µg of total RNA per sample, but we can work with much less. We have successfully tested the use of very small samples, and can discuss the possibilities and limitations of such experiments; do not pool samples before consultation. We need basic information about the samples before we receive them. A form for entering the information, and a brief explanation, can be downloaded.

Pricing is per sample, and includes the cost of the GeneChips; chips must usually be ordered in even numbers. GeneChips are purchased and stocked by the Center. To insure high quality, we do not hybridize or scan samples processed by others. The Center for Medical Genomics carries out the labeling, hybridization, washing and scanning of the array, and provides data to the investigators. We can also assist with data analysis and interpretation- discuss this with Drs. McClintick or Edenberg.

We have the most recent Affymetrix GeneChip Scanner 3000, capable of scanning all current Affymetrix GeneChips.

Examples of Gene Expression Arrays (*must be purchased in sets of 2, 6 or 30; †must be purchased in sets of 5 or 30)

GeneChip® Human Genome U133 Plus 2.0*
GeneChip® Rat Genome 230 2.0 Array*
GeneChip® Mouse Genome 430 2.0*
GeneChip® Rhesus Macaque Genome Array*
GeneChip® Drosophila Genome 2.0 Array*
GeneChip® Bovine Genome Array*
GeneChip® Chicken Genome Array*
GeneChip® Porcine Genome Array*
GeneChip® Canine Genome 2.0 Array*
GeneChip® Plasmodium/Anopheles Genome Array
GeneChip® Yeast Genome 2.0 Array*
GeneChip® E. coli Genome 2.0 Array*
GeneChip® Maize Genome Array*
GeneChip® Xenopus Genome Array†
GeneChip® Zebrafish Genome Array†
GeneChip® C. elegans Genome Array†
GeneChip® Arabidopsis ATH1 Genome Array†Human Genome Arrays

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The Center for Medical Genomics is partially supported by a competitive, peer-reviewed grant from the State of Indiana 21st Century Research and Technology Fund. Additional support is from the Indiana Genomics Initiative, funded by a generous grant from the Lilly Endowment, and from the Indiana University School of Medicine.