Additional file 3 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

Additional file 3: Genetic sex of RNA-Seq samples when aligned using STAR. Gene expression log2(CPM + 0.25/L) for select XY homologous genes (DDX3X/Y, PCDH11X/Y, USP9X/Y, ZFX/Y, UTX/Y) and XIST and SRY when reads were aligned to a default reference genome A), and for B) when reads were aligned to a sex chromosome complement informed reference using STAR. Male XY whole blood, brain cortex, breast, liver, and thyroid samples are shown in blue squares and female XX in orange circles.