Sensitive Platform

Findings from the first ever systematic comparison of tiling microarray platforms showed the Roche Nimblegen Chip chip arrays for Encode (Encyclopedia of DNA Elements) studies to be the most sensitive platform detecting genome-wide, protein-DNA interactions. This study revealed that microarrays employing longer oligonucleotide probes (50mers) are the most sensitive at detecting very low enrichment in simulated ChIP-chip experiments. As shown in the recently published, first objective analysis of tiling array platforms, DNA amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment by Johnson et al in Genome Research, the arrays are the most sensitive platform at lower levels of enrichment. Predetermined DNA sequences were used to imitate chromatin immunoprecipitation experiments. The DNA sequences were not disclosed to the participating researchers in order to prevent a biased evaluation of each tiling array platform.