Supplementary Figure 3: Validation of transcriptional responses in MSL3 patients.
a, MA plot comparing the mean of the normalized counts versus the log2[fold-change] obtained from RNA-Seq of patients versus Control (ctrl) HDFs (n = 2 passages of Control were compared with n = 2 passages of P1, P2 and P14 each). DE genes (FDR cutoff of 0.05) are marked in red. b, H4K16ac ChIP–qPCR analysis of H3F3B and respective expression levels from RNA-Seq (normalized read counts) displayed as dot plots. H4K16ac ChIP–qPCR enrichment values were calculated relative to input and expressed as a fold change enrichment over the negative control, KLK3. Each data point represents an independent experiment (n) with the center line representing the mean ± s.e.m. where applicable. c, RT–qPCR expression analysis in HDFs displayed as dot plots. Expression levels were normalized to RPLP0 and expressed relative to Control (ctrl). Each data point represents an independent experiment (n) with the center line representing the mean ± s.e.m. where applicable. P values were determined by ordinary one-way ANOVA followed by Bonferroni multiple-test correction. Further details and statistical test values are provided in Supplementary Table 5. d, Immunohistochemistry for the serotonin receptor HTR7 and netrin receptor UNC5B on Control (ctrl) and patient-derived FFPE skin sections. Similar staining results were obtained in n = 2 sections per slide. e, RT–qPCR expression analysis in male and female HDFs upon MSL3 knockdown (KD) displayed as bar plots representing the mean ± s.e.m. Expression levels were normalized to RPLP0 and expressed relative to scrambled siRNA (scramble). The same data points for ZNF185 and SPON2 are also shown in Fig. 3 and are illustrated again for comparative purposes. Each overlaid data point represents the number (n) of independent experiments.
