Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

ABSTRACT: A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or mis

SUBMITTER: Guertin MJ 

PROVIDER: S-EPMC6093181 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature