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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states

Fig. 4

Completely skewed X inactivation in B6D2F1 EpiSCs. a Tag-normalized RNA-seq data over Xist gene. b Quantification of Xist expression (RPKM), including allelic bias for the EpiSCs. Expression of Xist in the ESCs is too low to quantify allelic bias. c Distribution of relative expression of genes from the B6 versus the DBA2 allele in the ESC and EpiSC lines over chromosome X or autosomes (control). A log2 ratio of 0 represents equal gene expression from the B6 and DBA2 alleles, while positive and negative ratios represent higher expression from the B6 or DBA2 allele, respectively. On top the number of genes included in each of the boxplots, for the PGA lines we only included genes in the heterozygous B6/DBA2 parts. Besides ESC-NT1, EpiSC2 and EpiSC3, all lines are female. Note that the EpiSC-PGAs contain a largely heterozygous X chromosome including the Xist locus, enabling allele-specific RNA-seq calls (Additional file 4: Table S3). d B6/DBA2 ratio per gene over the linear X chromosome (the X-axis represents genomic coordinates in MB). Each dot represents a gene, and 50 genes had sufficient coverage over SNPs to be included. In blue (for female EpiSC1 and EpiSC-NT1) the B6/DBA2 ratio obtained by DNA sequencing at 5 MB resolution, confirming the presence of a B6 and DBA chromosome X in both lines. Additional file 2: Fig. S18 includes the same graphs for all B6D2F1 fertilized and NT ESCs or EpiSCs included in this study. e Distribution of gene expression in ESC and EpiSC lines over chromosome X or autosomes (control). The lower expression of X-linked genes in EpiSCs as compared to ESCs is the consequence of XCI in the EpiSCs resulting in dosage compensation between expression of autosomes and chromosome X. Genes with an expression level of RPKM > 2 in all ESC (246 and 8416 genes on chromosome X and autosomes, respectively) or EpiSC lines (332 and 9382 genes on chromosome X and autosomes, respectively) are included in this analysis

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