Expression Analysis (Illumina BeadChip)

illumina-beadchips2Our Core facility supports the use of the Illumina bead-array based gene expression platform for studies in human 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 – the Illumina iScan – used for SNP genotyping.  Economy is manifested through scale in the Illumina platform. The “BeadChip” array format used by Illumina uses 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.

HumanHT-12 v4 Expression BeadChip: 12 samples/chip (2 chips/pack) each representing > 47,000 probe sequences derived from RefSeq genes (NCBI RefSeq Release 38, November 7, 2009) and the latest Unigene release for genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants.

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.

Illumina BeadChip Arrays provide a highly consistent, economical gene expression array platform.

How to Access this Technology

For more information about running Illumina expression arrays through our facility, download this informational document.

Please contact Siranoosh Ashtari for sample submission details; Our policy is that we don’t order the arrays for your experiment until we have this completed 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. 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 using Bioconductor or other programs are beyond the scope of our facility.