Figure 4. Context-dependent NANOG binding in ESCs/EpiLCs.
a, qPCR analysis; induction of Prdm1/Prdm14/Tfap2c by Nanog (+Dox) in EpiLCs; ΔΔCt +/− s.d. (n=3 technical replicates each from 2 biological replicates).
b, Genome-wide NANOG binding in D2 EpiLCs 3h after Nanog (+Dox). ‘Distal’ intergenic’ peaks: +/−50kb of coding gene, and those further away designated as ‘intergenic’.
c, NANOG ChIP-seq in ESCs and D1/D2 EpiLCs, with specific or shared high-confidence peaks; n=2 biological replicates.
d, ChIP-seq tracks9,30 at Prdm1 and Prdm14 loci, with putative enhancers (boxed) analysed in (e-g). RPM = Reads per Million.
e, Analysis of Prdm1 enhancer-luciferase reporter in ESCs, EpiLCs, and after PGCLC induction (+Dox, EpiLC aggregations, unsorted). Mean luciferase activity normalised to protein quantity (luc/pro) +/− s.d. (n=3 technical replicates). Reference for p-value (two-sided/unpaired t-test): EpiLC aggregations −Dox; **p<0.01; *p<0.05. Controls and replicates in Extended Data Fig. 10c, e.
f, SOX2 ChIP-qPCR in ESCs and 6h after PGCLC induction +/−Dox (+/−Sox2) (unsorted EpiLC aggregations). Mean of fold enrichment over negative region +/− s.e. (n=2 technical replicates each from 2 biological replicates); reference for p-values (two-sided/unpaired t-test): IgG; *p<0.05.
g, Analysis of Prdm14 enhancer-luciferase reporter in ESCs, EpiLCs and after PGCLC induction (+Dox, EpiLC aggregations, unsorted). Mean luciferase activity normalised to protein quantity (luc/pro) +/− s.d. (n=3 technical replicates); reference for p-values (two-sided/unpaired t-test): EpiLC aggregations −Dox 24h; **p<0.01. Colour code as in (e); controls and replicates in Extended Data Fig. 10c, e.