title: H3K4me3 chIP-seq for AC7643 (IP). Not Stressed. Replicate I.
design: H3K4me3 profiling was performed on two replicates of the roots from drought tolerant inbred line AC7643 seedlings using antibodies specific for H3K4me3 (Ab8580, Abcam) according to manufacturers recommendations as previously described (Ye et al. 2016). In brief, 1% formaldehyde was used to crosslink protein-DNA interactions and chromatin was then sheared to an average size of around 350 bp. Half of the sonicated sample was immunoprecipitated with anti-H3K4me3 antibodies and the other half was not added any specific antibody but pre-immuneserum. After overnight incubation at 4 C, the antibodies-protein/DNA complexes were isolated using Protein A/G magnetic beads (Pierce) and the ChIP-ed DNA was isolated by reverse crosslinking with proteinase K and purified using PCR purification columns (Qiagen). The ChIP-ed DNA was subsequently processed with A-tailing, adaptor ligation, and library amplification steps using the NEBNext? Ultra? II DNA Library Prep Kit (NEB). The library was sequenced on an Illumina HiSeq 3000 instrument with 2  150 bp reads in Beijing Genomics Institute (Shenzhen, China). The procedures for H3K36me3 were the same but with different antibodies (H3K36me3: Ab9050, Abcam).