GSM7316596: HS, input, rep1; Arabidopsis thaliana; ChIP-Seq
Plants were then frozen in liquid Nitrogen and ground using a bead shocker (MB1200 Yasui Kikai) in 50 ml tubes ﻿and the nuclear fraction was isolated after cross-linking for 10 min using 1% formaldehyde (Sigma) under vacuum. 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. Sheared chromatin was immunoprecipitated using antibodies against GFP (ab290, Abcam) and input DNA was kept as a control. ﻿The isolated DNA was quantified with the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific), and 1–5 ng of DNA was used to make each ChIP-seq library. Libraries were prepared using the KAPA Hyper Prep Kit for Illumina (KK8502, KAPA Biosystems) and Illumina compatible adaptors (E7335, E7500, E7710, E7730, NEB). The 300–500 bp DNA fragments were enriched using Agencourt AMPure XP (Beckman Coulter). Libraries were pooled and 50-bp, single-read sequences were obtained with Illumina NextSeq500 sequencer at a depth of at least 10 million mapped reads.