ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

ABSTRACT:

Background

Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster.

Results

Both technologies produce

SUBMITTER: Ho JW 

PROVIDER: S-EPMC3053263 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature