title: H3K4me1 Histone modification of rice
design: Construction of ChIP-seq libraries was according to the protocol of “preparing samples for ChIP sequencing of DNA” provided by Illumina. Briefly, ChIPed DNA was end repaired using ‘End-It DNA End Repair Kit’ (Epicentre, ER0720). The ‘dA’ base was then added to the 3’ ends of the blunt-ended DNA fragments using Klenow fragment (3’-5’exo-) (NEB, M0212S). Linker for single read was ligated to the DNA molecules with ‘dA’ overhang using LigaFast kit (Promega, M8221). After 2% agarose gel running with TAE buffer, the gel region containing about 150-300 bp DNA was excised for adapter ligated DNA size selection. The adapter modified DNA fragments were enriched by PCR and purified by running 2% agarose gel in TAE buffer for isolation of DNA fragments in the range of 200-300 bp. The purified DNA sample was ready for Illumina sequencing after quality validation. ChIP libraries were prepared for sequencing using standard Illumina protocols