Figure 1.

XACT and XIST Are Co-expressed in the Early Stages of Human Development

(A) Principal component analysis illustrates the developmental trajectory within the two datasets used in this study, based on the n = 1,000 most variant GENCODE genes within each dataset.

(B) Boxplot of XACT and XIST expression levels (log2 FPKM) according to developmental stage, from dataset 1.

(C) Upper panel: plot of XACT versus XIST expression levels (log2 reads per kilobase per million mapped reads [RPKM]) in early-stage female cells of dataset 2 (E3, E4, and early E5), with corresponding Spearman correlation score and p value. Lower panel: distribution of Spearman correlation scores between XIST and each X-linked gene expression level. The median correlation score is indicated as a blue dashed line and a red line indicates the correlation score with XACT expression levels.

(D) Plots of XACT versus XIST expression levels (log2 RPKM) in late-stage female cells of dataset 2 (E5, E6, and E7), in trophectoderm (left panel) and epiblast and primitive endoderm cells, as assessed by a 75-gene signature shown in Figure S1C. The corresponding Spearman correlation score and p value are indicated.

(E) Boxplot of the number of X-linked bi-allelic positions normalized by coverage according to day of development for dataset 2. The p values of a Wilcoxon rank test comparing distributions between stages are indicated above the boxplot.

(F) Boxplot of the number of X-linked bi-allelic positions normalized by coverage for XACT-positive and -negative cells in female late-stage blastocysts. The p value of a Wilcoxon rank test comparing both distributions is indicated above the boxplot.