Fig. 3

Allele-specific RNA-seq reveals differential sensitivity of Xi genes to reprograming-mediated reactivation. a Summary scheme showing the relative positions of human Xi genes that are significantly expressed before and after reprogramming in clones 12 or 34 (purple), are reactivated (green) or that remain inactive (red) upon reprograming; analysis based on allele-specific RNA-seq of reciprocal hF clones 12 and 34 (i.e. X₁aX₂i or X₁iX₂a; see Fig. 1a). b–d Histogram plots show the % of minor allele (Xi) vs. total SNP-reads per gene, as assessed by RNA-seq analysis (mean ± SEM of two biological replicates for each clone). SNPs with the lowest number of overlapping reads in hF clone 12 were considered to be Xi alleles (and to be Xa alleles in reciprocal clone 34). Asterisks (*) mark samples showing significant expression from Xi allele in replicate merged data (probability of inactivation τ_i0 < 0.05, β-binomial statistics). Complete dataset analysis is reported in Table S3