NextSeq 500 paired end sequencing; RNAseq of mESC expressing different epigenetic editing machineries
Naïve murine embryonic stem cells (mESC) were derived freshly (FVB or mixed 129/B6)  and were routinely cultured on gelatin-coated plates in t2i/L media: NDiff (N2B27) (Takara #y40002) supplemented with titrated 2i (0.2 μM PD0325901 and 3 μM CHIR 99021), 1,000 U/ml leukaemia inhibitory factor (LIF), 1% FBS, 1% penicillin streptomycin and maintained in humidified atmosphere at 37°C and 5% CO2. Cells were passaged every 2 days by dissociation with TrypLE and medium was changed daily. Total RNA was isolated from cell pellets using NEB Monarch® Total RNA Miniprep Kit and libraries prepared using NEBNext RNA Ultra II kit (NEB E7770S, input: 350 ng of total RNA). RNA-sequencing of polyA RNA from mouse Embryonic Stem Cells. Total RNA was isolated using the Monarch® Total RNA Miniprep Kit (NEB #T2010S), including gDNA removal step and on-column DNase I digestion. Total RNA was quantified using Qubit III and quality assessed with high-sensitivity RNA Screen Tape (Agilent 5067-5579). Stranded mRNA-seq libraries were prepared with the NEBNext RNA Ultra II kit (input: 350 ng of total RNA) following the manufacturer's instructions.