title: Sox2_KO_EarlyICM_1
design: 20 to 40 morulae or ICMs were pooled and lysed in the lysis buffer (10 mM TrisHCl, pH=7.4; 10 mM NaCl; 3 mM MgCl2; 0.15% Igepal CA-630; 0.1% Tween-20) for 10 min on ice. We added 0.1% Tween-20 to the lysis buffer as it greatly reduced reads mapped to mitochondrial DNA. Lyzed embryos were briefly washed, collected in 2.0 l PBS containing 0.1 mg/ml polyvinyl alcohol (PVA) and transferred to 3.0 l Tn5 transposome mixture (0.25 l Tn5 transposome, Illumina, FC-121-1030; 2.5 l tagmentation buffer, 0.25 l H2O). The samples were incubated in 37 C water bath for 30 min. Tagmentation was stopped by adding 2.0 l stop buffer (175 mM EDTA) and incubated at 50 C for 30 min. Excess EDTA was quenched by 2.0 l quench buffer (160 mM MgCl2). The libraries were amplified in the following reaction: 9.0 l Transposed DNA, 10.0 l NEBNext High-Fidelity 2PCR Master Mix (New England Biolabs, M0541S), 0.25 l 100 M PCR Index 1, 0.25 l 100 M PCR Index 2 and 0.5 l H2O. The sequences of index 1 and 2 are in Table S3. The PCR program is as the following: 72 C for 5 min; 98 C for 30s; 16 thermocycles at 98 C for 10 s, 63 C for 30 s and 72 C for 1 min; followed by 72 C 5 min. Amplified libraries were purified twice with 1.2  AMPure XP beads.