The cells were trypsinized and washed prior to encapsulation To minimize the abundance of barcode adaptors concatemers we use PacI restriction enzyme (R0547L, NEB, USA) immediately after ChIP washing steps and while the chromatin is still bound to the ChIP beads. PacI digest in between bound concatemers and in the middle of each adapter to form 30bp DNA fragments that can be easily filter out using simple size selection. Next, we elute the chromatin by adding 2X elution buffer, digesting RNA contaminates with Rnase (11119915001, Roche Diagnostics, USA) and removing the nucleosomes with ProtenaseK (P8102S, NEB, USA). To purify the DNA we use AMPure XP beads (A63880, Beckman Coulter, USA) and follow with 14 rounds of Single-Cell-PCR to amplify the labeled DNA. To reduce unspecific Illumina adapter ligation we first dephosphorylate all 5’ ends with Antarctic Phosphatase (M0289L, NEB, USA) and then use BciVi enzyme (R0596L, NEB, USA) to specifically cleave the labeled DNA, leaving an A overhang at the 5’ end of all DNA fragments with single cell adapters. After ligating Illumina adapters, we digest concatemers again using PacI and perform 14 additional rounds of Illumina-PCR (PfuUltra II Hotstart PCR Master Mix, 600850, Agilent Technologies, USA) before sequencing the library of reads. Size selected for 200bp-1000bp