Supplementary Figure 1: Reproducibility of H3K27ac ChIP-seq
From: Genome-wide identification and characterization of functional neuronal activity–dependent enhancers
(a) Reproducibility of H3K27ac ChIP-seq signal (no KCl treatment) at individual H3K27ac peaks genome-wide between two biological replicate samples, with the ChIP performed independently for each biological replicate (ρ = 0.91, Spearman’s rank correlation coefficient). H3K27ac peaks were identified by MACS (MACS default parameters; p = 1 X 10–5). (b) Reproducibility of H3K27ac ChIP-seq signal (2 h KCl treatment) at individual H3K27ac peaks genome-wide (ρ = 0.94, Spearman’s rank correlation coefficient). (c) H3K4me1 ChIP-seq signal at gene distal DHS sites enriched for H3K27ac before and after 2 h membrane depolarization by KCl (ρ = 0.96, Spearman’s rank correlation coefficient). (d) H3K27ac ChIP-seq signal at gene distal DHS sites enriched for H3K27ac before and after 2 h membrane depolarization by KCl (ρ = 0.77, Spearman’s rank correlation coefficient). (e) Classification of gene distal DHS sites with distinct H3K27ac dynamics in response to neuronal activity (see methods).
