Extended Data Fig. 10: Network analysis of formative gene regulation by Esrrb.
From: Esrrb guides naive pluripotent cells through the formative transcriptional programme
a: Barplot showing expression of Otx2 measured by qPCR in ES cells treated for 48 h with ActivinA (20 ng/ml), FGF2 (12.5 ng/ml) and inhibitors of TGF-beta (A83-01, 1 μM) and FGF signalling pathways (PD173074, 0.5 μm). Cells cultured in 2iL or N2B27 for 48 h were used as controls. Mean +/−SD of n = 3 independent biological replicates (dots) are shown. b: Genome browser snapshot of histone modifications at Otx2 enhancer (E) bound by Esrrb and promoter (P), in naive and formative cells. Profiles are the integration of n = 2 biological replicates. c: ABN derived from a Pearson correlation threshold of 0.56 (see Methods). Solid black lines indicate required and definite interaction, dashed lines indicate optional interactions, red lines indicate disallowed interactions. Positive regulations are indicated by a black arrow, negative regulations are indicated by a black circle-headed line. d: Summary of 4 experimental constraints, each with initial (left column) and final (right column) conditions. Gene expression is discretized as high (blue) or low (white).
