Supplementary Figure 1: Quality control and gene body analysis.

(A) Quantification of the recovered DNA after H3K9ac, H3K27ac, and H3K27me3 chromatin immunoprecipitation; IgG were used as negative control. Data is expressed as percentage with respect to Input (mean+s.e.m. of N=3 independent experiments, Pvalue: two-sided paired Student’s t-test; full statistics in Supplementary Data 15). (B) Heatmap of the ATACseq signal in each sample, as FPKM of reads within 1Kb of TSS of each gene, filtered for genes that are significantly DA after either SNA vs sham, or DCA vs lam. Colour is scaled by row (gene) with blue representing the lowest signal and red representing the highest signal. Clustering was performed using a Euclidean distance function. (C) Heatmaps showing genomic distribution of ATACseq signal, as Log₂(Enrichment vs Background) (left) and H3K9ac, H3K27ac, and H3K27me3 histone mark signal, as Log₂(IP vs Input) (right) in the Laminectomy control sample. (D) Line chart of the correlation in sham between the chromatin accessibility and the occupancy of the indicated histone marks in the gene body (percentile epigenetic signal, mean of N=3 for ATACseq, and N=2 for ChIPseq, independent samples) and the gene expression level (Log₂FPKM, mean of N=3 independent samples); genes were divided in quartiles according to their expression level; Pvalue: 2-way ANOVA, Tukey’s multiple comparison test of the histone mark and ATAC signal in each quartile compared to the preceding one (ns=not significant); (full statistics in Supplementary Data 15). (E) Stacked bar plot of the number of genes with a differential occupancy of the indicated histone marks and chromatin accessibility at gene body upon SNA vs sham, or DCA vs lam (N=2 for ChIPseq, and N=3 for ATACseq, independent samples; Pvalue<0.05). (F) Area-proportional Venn diagram of the genes showing an increased H3K9ac and H3K27ac occupancy at both the TSS at gene body (N=2 independent samples; Pvalue<0.05). (G) Scatter plots of the histone mark occupancy in FPKM at the TSS (+−/1Kb) for the genes with increased (red dots) or decreased (blue dots) chromatin accessibility (N=3 independent samples; Pvalue<0.05).