For RNA-Seq, mRNA was specifically enriched from total RNA using oligo(dT) beads and sheared into small pieces.  The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis using DNA polymerase I.  The short cDNA strands were ligated with 3' and 5' adapters for amplification and sequencing.  For ChIP-seq, uninduced control and induced knockdown cells were crosslinked with 1% formaldehyde and chromatin was disrupted into 100-400 bp fragments by sonication and precipitated with either anti-uH2B or anti-H2B antibodies.  After elution from the beads and reverse cross-linking, the DNA fragments were extracted with phenol/chloroform and recovered by ethanol precipitation.  Immunoprecipitated DNA was ligated with 3' and 5' adapters for amplification and sequencing.
GEO Accession
GSM1165981