Chromatin immunoprecipitation (ChIP) followed by tag sequencing (ChIP-seq) using high-throughput next-generation instrumentation is fast, replacing chromatin immunoprecipitation followed by genome tiling array analysis (ChIP-chip) as the preferred approach for mapping of sites of transcription-factor binding and chromatin modification. Using two deeply sequenced data sets for human RNA polymerase II and STAT1, each with matching input-DNA controls, we describe a general scoring approach to address unique challenges in ChIP-seq data analysis.
Regulated genes (or markers): 13082
Regulatory sequences (genomic): 36902
Regulatory sequences (artificial): 0
Transcription factors: 1
Transcription factor profiles: 0
Annotated publications: 1
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