Tiling Array - Procedure

Procedure

Several different methods exist for tiling an array. One protocol for analyzing gene expression involves first isolating total RNA. This is then purified of rRNA molecules. The RNA is copied into double stranded DNA, which is subsequently amplified and in vitro transcribed to cRNA. The product is split into triplicates to produce dsDNA, which is then fragmented and labeled. Finally, the samples are hybridized to the tiling array chip. The signals from the chip are scanned and interpreted by computers.

Various software and algorithms are available for data analysis and vary in benefits depending on the manufacturer of the chip. For Affymetrix chips, the model-based analysis of tiling array (MAT) or hypergeometric analysis of tiling-arrays (HAT) are effective peak-seeking algorithms. For NimbleGen chips, TAMAL is more suitable for locating binding sites. Alternative algorithms include MA2C and TileScope, which are less complicated to operate. The Joint binding deconvolution algorithm is commonly used for Agilent chips. If sequence analysis of binding site or annotation of the genome is required then programs like MEME, Gibbs Motif Sampler, Cis-regulatory element annotation system and Galaxy are used.