Oct4, Sox2 and Nanog cooperate to form the transcriptional regulatory circuitry of embyronic stem cells. To gain insight into the genes regulated by the core circuitry of transcription factors, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets of Oct4. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against IgG as a background control. ChIP was performed using an antibody against Oct4 in two biological replicates. The first replicate was sequenced twice (technical replicate 1 and technical replicate 2).