Systematic evaluation of variability in simulated ChIP-chip experiments Kevin_Encode

ABSTRACT: The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance

ORGANISM(S): Homo sapiens

SUBMITTER: Wei Li 

PROVIDER: E-GEOD-9848 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress