title: ampDAP-seq of Marchantia polymorpha (BoGa): Mp2g08360
design: ampDAP-seq was executed as previously described in the publication of Bartlett et al. 2017 with minor modifications. In brief, gDNA from Marchantia polymorpha subsp. ruderalis BoGa was isolated using the CTAB method and was fragmented to 200 bp by sonication with the M220 Focused-Ultrasonicator (Covaris, USA). End-repair, A-tailing and Y-adaptor ligation were performed for the DAP-library. Instead of ethanol precipitation, DNA was purified using AMPure XP beads (Beckman Coulter, USA). For ampDAP library, 15 ng of the DAP library was amplified (11 PCR cycles). Binding assay: genes were cloned in pFN19A (HaloTag7) T7 SP6 Flexi vector (Promega, USA) applying Gibson assembly (Gibson et al., 2009). Expression of Halo-tagged TFs was performed on 2 g plasmid DNA using with TnT Coupled Wheat Germ Extract System (Promega, USA). Proteins were immobilised with Magne HaloTag Beads (Promega, USA) and incubated with ampDAP library (50 ng). DNA was then recovered, amplified and indexed (20 PCR cycles). QIAquick Gel Extraction Kit (Qiagen, Netherlands) was performed to extract DNA fragments (200-400 bp) from an 1% agarose gel. Final library was sequenced on a NextSeq 550 (Illumina, USA) as 85 bp long single-end reads.