H3 profiling by ChIP-Seq in 7d autotrophic shoot, rep3
Sample was crosslinked using 1% formaldehyde for 10 min under vacuum, terminated using 0.125 M glycine for 5 min and flash frozen for ChIP. Sheared chromatin (10 cycles, 30 s ON/ 30 s OFF using a Bioruptor® (Diagenode)) was divided in samples immunoprecipitated with anti-histone H3 (Merck, cat. no. 07-690). Immunocomplexes were collected using Dynabeads® Protein A for Immunoprecipitation (Thermo, cat. no. 10001D) and washed 2 x 5 min with low-salt buffer (containing 150 mM NaCl), 2 x 5 min with high-salt buffer (containing 500 mM NaCl) and 1 x 5 min with LiCl-containing buffer. Immunoprecipitated DNA was purified using iPure kit v2 (Diagenode, cat. no. C03010015). Illumina sequencing library preparation was done using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEB, cat. no. E7645S).