Illumina BeadChips

http://www.dkfz.de/gpcf/beadchips.html

mouseWG-6 v2 BeadChip®

The BeadChip Mouse Sentrix-6 V2 offers comprehensive analysis of genome-wide expression on a single array.

* probes are defined gene-specific 50mer oligonucleotides
* >700,000 oligonucleotides per bead/spot
* on average 30x redundancy for each transcript
* Provides comprehensive coverage of the transcribed mouse genome on a single array
* Analyzes the expression level of 45,281 mouse transcripts, variants, and EST clusters
* comprised of more than 1,600,000 beads per chip
* Up-to-date gene list and annotation of Mouse Sentrix-6 V2 BeadChip

For more information please download the Mouse Sentrix-6 V2 Whole Genome BeadChip datasheet and the corresponding technical bulletin from Illumina. One physical array is made up of 6 identical, but independent chips.

http://www.ohsu.edu/xd/research/research-cores/gmsr/project-design/array-technology/illumina-bead-arrays.cfm


The Illumina BeadChip is proprietary method of performing multiplex gene expression and genotyping analysis. The essential element of BeadChip technology is the attachment of oligonucleotides to silica beads. The beads are then randomly deposited into wells on a substrate (for example, a glass slide). The resultant array is decoded to determine which oligonucleotide-bead combination is in which well. The decoded arrays may be used for a number of applications, including gene expression analysis and genotyping. Scroll to the bottom of the page for a primer on array decoding.
Expression array overview

Gene expression analysis is performed using a 79-base oligonucleotide that has two segments. The 5′ 50-base segment of the oligonucleotide is designed to hybridize to sequences available in the public data repositories. It is this segment that will bind to the labeled target derived from the poly(A) component of the total RNA. The 3′ 29-base segment of the oligonucleotide is the address. The address is a unique sequence created by Illumina specifically to allow unambiguous identification of the oligonucleotide after it has been deposited on the array.

Illumina_schematic

Arrays may have as many as 44,000 unique oligonucleotides. Each oligonucleotide is synthesized in a large batch using standard technologies. The oligonucleotides are then attached to the surface of a 3-micron silica bead. Each bead has only one type of oligonucleotide attached to it, but it has hundreds of thousands of copies of this oligonucleotide.

Standard lithographic techniques are used to create a honeycomb pattern of wells on the surface of glass slides. Each well can hold one bead. The beads for a given array are mixed in equal amounts and deposited on the slide surface. The beads occupy the wells in a random distribution. Each bead is represented by, on average, about 20 instances within the array. The identity of each bead is determined by decoding using the address sequence. A unique array layout file is then associated with each array and used to decode the data during scanning of the array.