title: GSM8016847: PHYD-YFP/ab-C-de, 5 minutes, rep 2; Arabidopsis thaliana; ChIP-Seq
library_construction_protocol: The ChIP protocol by Werner Aufsatz (https://www.epigenome-noe.net/researchtools/protocol.php_protid=13.html) was applied with the following modifications. Chromatin samples were sonicated on ice six times for 10 s using a Vibra Cell sonicator (SONICS & MATERIALS Inc., Danbury, CT, USA) at 10% power. Sonicated and diluted chromatin samples were pre-cleared by 20 µl (bed volume) of binding control agarose beads (Chromotek GmbH, Germany) for 1 h at 4 °C. Chromatin was precipitated using 12.5 µl (bed volume) of GFP-Trap agarose beads (Chromotek GmbH, Germany) for 16 h at 4 °C. Precipitated chromatin was eluted from the beads, de-crosslinked and DNA was extracted using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel, Düren, Germany) with Buffer NTB (Macherey-Nagel, Düren, Germany). Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) along with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2, New England BioLabs) according to the manufacturer's protocol. Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation 2200 (all from Agilent); quantification was performed using Qubit dsDNA BR Assay kit (Thermo Fischer Scientific). Sequencing was performed on Illumina NextSeq 1000 instrument.