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Illumina Gene Expression

Our core facility supports the use of the Illumina bead-array based gene expression platform for studies in human, mouse, or rat systems.  Advantages of this platform include the use of 50-mer probe sequences for better selectivity and sensitivity, greater than 30-fold feature redundancy for higher confidence fluorescent intensities, high feature density allowing smaller reagent and sample volumes, and standardized hybridization set ups for reproducible data generation.  (This procedure utilizes the same bead array reader used in our sister facility, the DNA Technologies Core). Economy is manifested through scale in the Illumina platform. The "BeadChip" array format used by Illumina utilizes either 6, 8, or 12 different arrays on a glass slide which are processed simultaneously. The per array cost is inexpensive, but it is clearly critical to fill each slide with labeled RNA target samples for the best value. The available array formats are:

Sentrix Human Ref-8 Expression BeadChip: 8 arrays/chip, each representing >23,000 sequences representing NCBI RefSeq genes. 

Sentrix Human-6 Expression BeadChip: 6 arrays/chip, each representing > 48,000 probe sequences derived from RefSeq genes and the latest Unigene release.

Sentrix HumanHT-12 BeadChip: 12 arrays/chip, each representing > 44,000 probe sequences derived from RefSeq genes and the latest Unigene release.  Most economical option, please inquire for pricing.

Sentrix Mouse Ref-8 Expression BeadChip: Similar layout to human Ref-8 (8 arrays, >25,000 probes/array), but derived from a combination of MEEBO oligonucleotides, RIKEN FANTOM sequences, and NCBI RefSeq sequences.

Sentrix Mouse-6 Expression BeadChip: Similar layout to human WG-6 (6 arrays, >48,000 probe sequences/array) from an expanded combination of MEEBO oligonucleotides, RIKEN FANTOM sequences, and NCBI RefSeq sequences.

Sentrix Rat Ref-12 Expression BeadChip: 12 array stripes/slide, >22,523 probes selected from NCBI RefSeq sequences (release 16).

For content information on these array types, visit the Illumina Website containing the gene lists and download the "Text Versions" for the format of interest. 

Gene expression data generated on Illumina platform at our facility:

 

Publications utilizing data generated on the Illumina platform at our facility:

Krig et al. Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays.

Xu et al. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members.

Cotterman et al. N-Myc Regulates a Widespread Euchromatic Program in the Human Genome Partially Independent of Its Role as a Classical Transcription Factor

How to access this outstanding technology

Illumina BeadChip Arrays provide a highly consistent, economical gene expression array platform.   For more information about running Illumina expression arrays through our facility, download this informational document.  If you want to see how well the Illumina platform stacked up in the unbiased analyses carried out by the Microarray Quality Control consortium, you can find out here. When you make the (wise) decision to run Illumina expression arrays with us, we ask that you fill out this submission form so that we can track your order more efficiently. NOTE:  this is a new form as of September 29, 2009 so please use this and not a previously downloaded version.  Our policy is that we don't order the arrays for your experiment until we have this form in hand.  Please follow all the instructions, and feel free to call or email if you have any questions.

Analysis with the Illumina platform

The results from an Illumina array experiment can be displayed (and exported) in a variety of ways, including essentially un-normalized fluorescent intensity data.  As part of the charge for our services, we can provide you with basic training on the Illumina software, and be available for a certain amount of initial consultation to help you navigate the different options and features of the program.  There is a worskstation containing the software available for use at no charge; additionally, we do have a certain number of software licenses but please inquire for more details.  Some normalization options and bioinformatic analyses can be carried out using the Illumina software, this chapter from the manual gives an idea of the basics provided.  Also, a recent paper from Dunning et al. provides an overview of analysis using the Illumina software and illustrates situations when users may want to carry out more detailed analyses through the use of Bioconductor resources.  Finally, we frequently are asked about guidelines for running and the utility of replicates.  Illumina provides a technical note regarding the use of replicates which can also be downloaded directly here for an initial discussion of this important topic.  More sophisticated experimental design information, statistical analyses, and array comparisons done using Bioconductor or other programs are beyond the scope of our facility.  However, we are committed to helping you get access to these resources so please inquire if this is of interest.