Supplementary Figure 9: Dataset validation.

(A) Spearman correlation analysis between DE genes after SNA vs sham, or DCA vs lam (N=3 independent samples; Pvalue<0.05 or FDR<0.05) and published datasets (GSE30165, GSE21007, GSE26350, and GSE33175) including several models of sciatic nerve injury at several time points as downloaded from Gene Expression Omnibus (GEO). SNL: sciatic nerve ligation. GSE number and time points after injury are reported for each dataset. Colour code indicates the degree and direction of the correlation (red=positive; blue=negative). Grey indicates not applicable analysis (no datasets available). The numbers in black represent the Pvalue by two-sided Fisher’s exact test (blank= not significant). (B) Odds ratio analysis of the enrichment of upregulated and downregulated genes in our dataset (Pvalue<0.05) across each upregulated and downregulated gene clusters of the individual published datasets; the numbers in red represent the Pvalue given by two-sided Fisher’s exact test (blank= not significant). (C) Bar plot of the number of DE genes in DRG after SNA vs sham, or DCA vs lam using specific significance cut offs (N=3 independent samples; Pvalue<0.05; FDR<0.1; FDR<0.05). (D-E) mRNA quantification by RT-PCR of the indicated transcripts upon SNA vs sham (D), or DCA vs lam (E) relative to control injury and normalized vs GAPDH (mean+s.e.m. of N=3 independent experiments for SNA (except N=5 for Hdac4); N=4 independent experiments for DCA (except N=3 for Hdac5; N=7 for Capn11); two-sided unpaired Student’s t-test; ns=not significant; full statistics in Supplementary Data 15). The red line represents a ratio=1, meaning no difference between conditions. (F) H3K27ac ChIP quantification by RT-PCR of the indicated promoter regions upon SNA or Sham injury normalized vs total H3 ChIP (mean+s.e.m. of N=3 independent experiments; two-sided unpaired Student’s t-test; ns=not significant; full statistics in Supplementary Data 15).