Extended Data Fig. 4: Allele-specific differential expression analysis of X-linked genes.
From: Escape from X inactivation is directly modulated by Xist noncoding RNA
a, MA-plots showing the results of a differential expression analysis in NPC clone E6 after 7 days of Dox treatment for X-linked genes considering reads from the Xa only, reads from the Xi only and total reads (including those not assignable to an allele) (n = 3 replicates per condition). P-values are computed using DESeq2 and FDR-adjusted. b, as (a), after 21 days of Dox treatment (3 replicates for control samples, 2 for Dox (21 d)). c, Heatmap showing the fold changes of X-linked gene expression after 7 days of Dox treatment for clone E6 as summarised in (a) for each gene individually. d, as (c), after 21 days of Dox treatment. e, as (c) for differentiated astrocytes. f-g, as in (c) for CL30 and CL31 respectively after 7 days of Dox treatment.
