FIG. 1.

XIST-positive and XIST-negative female hPSCs are transcriptionally similar, and distinct from male hESCs, regardless of XIST status. (A) XIST RNA FISH (red) in single class II XIST-positive (left) and class III XIST-negative (right) nuclei counterstained with DAPI (blue). Percentage of nuclei with an XIST RNA cloud is shown. (B) Unsupervised hierarchical clustering based on Minkowski distance of male hESCs (blue), female XIST-positive hPSCs (orange), and female XIST-negative hPSCs (pink). (C) PCA for all female and male undifferentiated hPSCs, with samples colored by cell type (left) and by XIST status (right). The percentage contribution of each PC is displayed in each axis. (D) Scatterplots of TPMs from XIST-positive compared with XIST-negative female hPSCs (top), XIST-positive hPSCs compared with male hESCs (middle), and XIST-negative hPSCs compared with male hESCs (bottom). hESCs, human embryonic stem cells; hPSCs, human pluripotent stem cells; PC, principal component; PCA, principal component analysis; RNA FISH, RNA fluorescence in situ hybridization; TPMs, Transcripts Per kilobase Million. Color images available online at www.liebertpub.com/scd