ChIP-Seq of mus musculus: H3K27acetylation
Preparation  of  sequencing  libraries  form  the  chromatin  immunoprecipitation  products  was performed with the MicroPlex Library Preparation system (Diagenode). The workflow for the library preparation consists of an end-repair step using 10 ng of immunoprecipitated (chipped) DNA prior to the ligation of Illumina-compatible adapters; qPCR was used to determine the optimal number of PCR amplification cycles (between 3 and 13 cycles) required to obtain a high  diversity  library  with  minimal  duplicated  reads  for  each  sample  prior  to  the  final amplification of indexed libraries and purification. The molarity of the libraries was assessed by  qPCR  using  the  KAPA  Library  Quantification  Kit  (Roche)  and  the  library  size  was determined on a LabChip GX Touch Nucleic Acid Analyzer (Perkin Elmer, Villebon-sur-Yvette, France) using the HT DNA High sensitivity chip (PerkinElmer). Indexed libraries were pooled and  normalized  to  4nM. Sequencing  was  performed  in  paired  end mode  (2  x  75  bp)  on the Illumina  HiSeq4000  platform.  The  targeted  histone  modification  (H3K27ac)  samples  were sequenced per lane, to obtain ~50-70 million reads/sample.