title: Nipponbare H3K9me2: Comparative transcriptome analysis among closely related rice strains
design: ChIP was performed as described (Zhu et al., 2012). Leaf tissue  (5g) from two-week old seedlings was fixed with formaldehyde and immunoprecipitated with anti-H3K4me3 (Millipore 07-473), anti-H3K9me2 (Cell signaling 4658S), or anti-IgG antibodies (Cell signaling 7074S).  After decross-linking and proteinase K and RNase treatments, immunoprecipitated DNA was purified by phenol/chloroform extraction. Eluted ChIPed DNA was used for library preparation per instructions (NEXTflexTM ChIP-Seq kit; BioScientific), and libraries were sequenced on the Illumina Hiseq 2500 platform. Yields of single-end reads of 100 bp for H3K4me3, H3K9me2 and IgG libraries were 35.1 million, 44.8 million, and 2.3 million respectively. Quality filtered reads were aligned to the Nipponbare reference genome (MSU7) with bowtie2 (Langmead and Salzberg, 2012) using default parameters so that non-unique reads from TEs could be aligned to a region randomly selected from multiple best hits. Peaks of H3K4me3 were called out by MACS software (Zhang et al., 2008). SICER software (Xu et al., 2014) was used to detect broad H3K9me2 signals.