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, For MNase the libraries were sequenced (PE150) by Novogene Co. Ltd. ChIP-seq was sequenced by the BioMics facility of the Institut Pasteur

, / Cell-cycle RNA-seq

, Around 10 6 cells were sorted per population before RNA extraction with 1mL TRIzol (ThermoFisher, Cat# 15596026), according to the manufacturer's protocol. To eliminate any genomic DNA contamination, this was followed by an additional DNAse I treatment (Qiagen, Cat# 79254) for 20min at 37°C followed by phenol:chloroform purification. RNAs were resuspended in Ultrapure DNAse/RNase Free Distilled Water (Thermo, Cat# 10977035). Ribodepleted, Ccna-GFP Sox2-AID ES cells were cultured in the presence of 0.5mM of auxin (Sigma, Cat# I5148) for 3 hours. During the last 20 minutes 20?M Hoechst-33342 was added

. /-western and . Blot,

, Cat# 161-0737) containing ?-mercaptoethanol. Lysed pellets were boiled for 10 min at 95°C and centrifuged for 10 min at maximum speed at room temperature. Typically, 10 µl per sample was loaded on 4-15% Mini-PROTEAN TGX Stain-Free Gels, Cat# 4568086) and run in 1× SDS-Running Buffer (250 mM Tris/ 1.92 M Glycine/1% SDS) at 10-20 mA using the Mini-PROTEAN Tetra System

, Tween-20) 5% BSA for 1 hour at room temperature and incubated over night at

, Membranes were washed 5 times, 10 min each at room temperature and incubated with PIERCE ECL2 Western Blotting Substrate (Thermo Scientific, Cat# 80196) 5 min in dark, Antibodies used: Primaries: anti-H3 (Abcam, Cat# ab1791) (1:5000), pp.500-501

, 8a/ Data and availability

, at least 2 x Interphase and 2 x Mitosis ChIP-seq samples were sequenced for DSG+FA ESRRB, SOX2, POU5F1, NANOG; for SOX2 RNA-seq 3 x (EG1, LG1, G2) x (-Auxin, +Auxin) samples were sequenced. For nucleosome positioning and accessibility data , 3 x (0.5U, 16U, 128U) x (Interphase, Mitosis) for MNase-seq, 3 x (0.5U, 16U, 128U) x (Interphase, Mitosis) for MNase H3 ChIP and 2 x (Interphase, Mitosis) for ATAC-seq, Samples are summarised in Table S1. Briefly

S. Esrrb and N. Chen, , 2008.

P. Sox2 and N. Fa-chip-seq-gse11724-(marson, , 2008.

P. Sox2 and N. Fa-chip-seq-gse44288-(whyte, , 2013.

. Sox2-fa-chip-seq-gse43275-(aksoy, , 2013.

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