TBP in mitotic bookmarking and reactivation of transcription [ChIP-Seq]

To test of TBP binds in the same genomic regions in mitosis compared to interphase cells, we performed Chromatin ImmunoPrecipitation coupled with sequencing (ChIP-seq). We used asynchronous mouse embryonic stem (ES) cells, or Nocodazole-synchronized mitotic ES cells as starting material for ChIP-seq. The cells were crosslinked with 1% formaldehyde, digested with MNase, and lightly sonicated to solubilize digested chromatin. This served as input for the ChIP. After extracting DNA from the ChIP experiment, we used paired end sequencing and mapped the reads to the mm10 genome. We then performed in silico size selection for reads under 100 bp and analyzed for enrichment at the TSS