Fig. 1

Identification and biological replication of sexually dimorphic genes in mouse ES cells. a, b Transcripts were defined as dimorphic from RNA-seq data using a genome-wide corrected FDR < 0.01 and standard deviation between biological replicates of less than 10%. Genes with sex-specific biases independent of strain are indicated on the y-axis. Sexually dimorphic expression in BC ES cells (a) showed clustering of the two XO lines with the three XY lines, separately and distinctly from the three XX lines. CB ES cells (b) showed clustering by sex chromosome complement with the three XY grouped together separately from the three XX lines. c Chromosomal distribution of sexually dimorphic genes when comparing all six XX and six XY ES cells at FDR < 0.01. d Principal component analysis (PCA) of differentially expressed genes at FDR < 0.01 from RNA -seq of ES cells shows distinct clustering of each cell line with close association of lines of the same strain and sex, with the exception of the two XO lines which highly overlap with the three XY lines of the same cross (BC). e Exclusion of sex chromosome-linked expression in the PCA at FDR < 0.01 shows maintenance of segregation of the ES lines based on strain and sex affirming that autosomal expression alone accounts for these biases