title: GSM3460553: input_DNA_FF_rep3; Mus musculus; ChIP-Seq
library_construction_protocol: For ChIP-seq, cells were crosslinked and chromatin was prepared according to a previous report (Nat. Protoc. 3, 1032-1045) with modifications. For RNA-seq, total RNA was purified using Isogen (Nippon Gene), and treated with DNaseI to digest genomic DNA. ChIP-seq libraries for H3K4me3, H3K27me3 and input (replicate 1 and 2) samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Libraries for H3K9me3 and input (replicate 3 and 4) were prepared using ThruPLEX DNA-seq Kit (Takara).  RNA-seq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).