GSM5696736: SOB3-GFP ChIP ZT4 replicate 1; Arabidopsis thaliana; ChIP-Seq
Frozen samples were ground to a fine powder using an MB1200 Multi-beads Shocker (Yasui Kikai). Ground tissue was mixed with nuclei isolation buffer and formaldehyde added to 1% final concentration. Fixation was stopped after 10 minutes by addition of glycine. Solution was filtered through miracloth and then centrifuged to pellet nuclei.  Pellet with nuclei was resuspended in nuclei isolation buffer, added on top of nuclei separation buffer containing 1 M sucrose, and then centrifuged to separate nuclei from debris. Nuclei were resuspended in SDS lysis buffer and incubated with rotation in order to lyse nuclei.  Subsequently, chromatin was sonicated in a Covaris S2 Focused-ultrasonicator (Covaris) to an average size of approximately 100-300 bp. Libraries were constructed from input or ChIPed DNA using the KAPA Hyper Prep Kit for Illumina (KAPA Biosystems) and Illumina compatible adaptors (New England Biolabs). Qubit dsDNA HS Assay Kit was used with the Qubit 2.0 Fluorometer (Invitrogen) for quantitation of DNA.