title: NextSeq 500 sequencing; Temporal dynamics of histone modification H3K9/14ac, H3K27ac, H3K4me3, H3K27me3, and H3K36me3 after wounding in Arabidopsis thaliana.
design: Temporal dynamics of histone modification H3K9/14ac, H3K27ac, H3K4me3, H3K27me3, and H3K36me3 after wounding in Arabidopsis thaliana.
library_construction_protocol: Samples were taken from roots of 7 days old plants in triplicates. Roots were cu into 3-mm explants at 0, 1, 3, 6 and 12 h after wounding,  Arabidopsis thaliana (ecotype Col-0) plants were grown on Murashige-Skoog (MS) media containing 1% sucrose and 0.6% (w/v) gelzan under continuous light conditions at 22°C. Root samples were ground to a fine powder using a multi-beads shocker (MB1200, Yasui Kikai) and the nuclear fraction was isolated after cross linking with 1% formaldehyde for 10 min. Chromatin was sheared at 4–6°C for 15 min with a focused ultrasonicator (Covaris) with the following settings: duty cycle 5%, intensity 4, and cycles per burst 200. Chromatin was immunoprecipitated using antibodies against H3 (ab1791; Abcam), H3K27me3 (07-449; Millipore), H3K4me3 (ab8580; Abcam), H3K36me3 (ab9050; Abcam), H3K9/14ac (06-599, Millipore) and H3K27ac (ab4729, Abcam).  DNA was extracted with phenol-chlorophorm (1:1), precipitated with ethanol and dissolved in TE.   Libraries were prepared using the KAPA Hyper Prep Kit for Illumina (KK8502, KAPA Biosystems) and Illumina compatible adaptors (E7335, E7500, E7710, E7730, NEB).