ATAC-seq libraries were generated as described previously (Buenrostro et al. 2013; Lara-Astiaso et al. 2014). Briefly, 10,000 freshly isolated cells (MPP, GMP, AML, and ES) were sorted by FACS into ice-cold FACS buffer (PBS + 2%FBS). The cells were pelleted using a swinging bucket centrifuge (500 x g, 10min, 4oC) with settings for low acceleration/deceleration and washed once in ice-cold PBS. The cell pellets were resuspended in 50μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) by gentle pipetting and immediately centrifuged one additional time (500 x g, 10min, 4oC). The supernatant was discarded and the pellet containing released nuclei were resuspended gently in 25μl 1xTD buffer containing 1.25μl Tn5 transposase (Nextera sample preparation kit, Illumina). The transposition reaction was allowed to proceed for 45min at 37oC whereafter DNA fragments were isolated using MinElute PCR purification columns (Qiagen) according to manufacturer's instruction. To generate multiplex libraries, the transposed DNA was initially amplified for 5x PCR cycles using 2.5μl each of dual-index primers (Nextera index kit, Illumina) and 2.5μl PCR primer cocktail (PPC, Illumina) in a 25μl reaction volume of 1x KAPA HiFi hot-start ready-mix (Kapa BioSystems). The hot-start polymerase was activated prior to adding to the reaction mix by performing a brief pre-incubation step of 3min at 95oC. The amplified fragments were size-selected with AMPure XP beads (0.5X) to remove fragments larger than 600bp and an aliquot was quantified to determine the optimal PCR cycle number to obtain 1/3 of maximum fluorescence intensity (Library quantification kit, Kapa Biosystems). Finally, PCR amplification was performed using the optimal number of cycles determined for each library (max. 18 cycles in total), size-selected with AMPure XP beads (0.5X) and eluted in resuspension buffer (Illumina). The size distribution of the libraries was evaluated on Bioanalyzer (Agilent) and sequenced on NextSeq 550 (Illumina) using 150bp or 75bp paired-end sequencing.