GSM1645416: RELA-60.; Mus musculus; RNA-Seq
Chromatin-associated RNA was biochemically purified as previously described (Bhatt et al, Cell 2012). Chromatin was resuspended in TriReagent and RNA purified using Rneasy columns (Qiagen). rRNA was depleted using the Ribominus Kit (Life Technologies). mRNA was isolated using TriReagent and RNA was purified using RNeasy columns (Qiagen). All chromatin and mRNA libraries were generated using the Illumina Truseq v.2 kit with a few modifications: strand specific libraries were generated using the dUTP method. Briefly, the second strand cDNA was synthesized in the presence of dUTP. Prior to library amplification, the second strand was degraded with dUTPase.