Fig. 3

Pluripotency and lineage-specific factors in XX and XY ES cells. a Fragments per kilobase per million (FPKM) values from RNA sequencing of six XX and six XY ES cells showing expression of 15 of the minimal network of pluripotency transcription factors. Two transcription factors were differentially expressed between the XX and XY cell lines: Tcf3 was 1.8-fold greater in XY, and Zfx was 1.5-fold higher in XX. *FDR < 0.05. b In the expanded pluripotency network, there are detectable and distinct differences in expression of key genes between XX and XY cells. Node size reflects the clustering coefficient and line thickness denotes the statistical significance of the interaction with arrows indicating a positive interaction and T bars indicating inhibition. Colors represent relative expression levels in RPKM for XX (left) and XY ES cells (right). c Differences in expression of lineage-specific markers. Note that expression levels were lower compared to levels of pluripotency-associated genes. The ectodermal lineage-specific marker Ncam1 was 2-fold higher in XX lines. The XY cells were enriched for Hand1, Cdx2, Eomes, Gata4, and T when compared to the XX lines with fold change of 2.6, 2.5, 2.4, 3.7, and 2.5, respectively. *FDR < 0.03