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PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M

Chromatin Immunoprecipitation followed by tag sequencing (ChIP-Seq) using high-throughput next-generation instrumentation is replacing ChIP-chip for genome-wide mapping of sites of transcription factor binding and chromatin modification, especially for mammalian genomes. Here we develop a methodology for identifying punctate binding sites in ChIP-Seq experiments based on their characteristics. In particular, we produce two deeply sequenced datasets for human RNA polymerase II and STAT1 with matching input DNA controls. In these sets, we observe that signal peaks, corresponding to sites of potential binding, are strongly correlated with peaks in input DNA that likely reveal features of open chromatin. Based on these observations we develop a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. Using our scoring approach we investigate the design of an optimal ChIP-Seq experiment. We examine the number of identified binding sites as a function of sequencing depth (i.e. saturation) and the value of multiple replicas. In particular, we find that little additional biological information is gained from more than two replicas.

Mappability Map <A href="" title="Mappability Map Code">Code</A>
Maps: <A CLASS="latinlink" href="" title="Map for C. elegans">C. elegans</A><A CLASS="latinlink" href="" title="Map for D. melanogaster">D. melanogaster</A><A CLASS="latinlink" href="" title="Map for H. sapiens">H. sapiens</A><A CLASS="latinlink" href="" title="Map for M. musculus">M. musculus</A>

ChIP-Seq Scoring <A CLASS="link" href="" title="Preprocessing Code">Preprocessing</A> <A CLASS="link" href="" title="C Code for ChIP-Seq Scoring">C Code</A> <A CLASS="link" href="" title="Perl Code for ChIP-Seq Scoring">Perl Code</A>

Scored results: <A CLASS="link" href="" title="Pol II Results">Pol II</A> <A CLASS="link" href="" title="STAT1 Results">STAT1</A>

Raw ChIP-Seq Sequence Data: <A CLASS="link" href = "" title="Pol II Sequence Data">Pol II</A> <A CLASS="link" href="" title="STAT1 Sequence Data">STAT1</A></P>

Contact Joel Rozowsky at joel DOT rozowsky AT yale DOT edu.

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