Figure 2.

Tbx3 Null mESCs Express an ESC-like Gene Expression Signature

(A) Tbx3 null mESCs maintain ESC-like morphology (top) and AP activity (bottom). Scale bars represent 200 μM.

(B) Single Tbx3 null mESCs sorted into 96-well plates and assayed for their ability to form AP-positive colonies. Data represent the average of two independent plates.

(C) Chimeric E10.5 embryos showing in vivo contribution of mESCs after blastocyst injection.

(D) mRNA levels of indicated ESC markers in mESCs cultured in the presence of LIF. Data are the average of three independent experiments. ^∗p < 0.05 (t test).

(E–H) Correlation of mESC-specific gene set between WT and Tbx3^N/N cells. Genes that have effects on mESC self-renewal from published genome-wide RNAi screens (E). Correlation of the same gene set between ESCs and EBs (G). Genes whose promoters are bounds by OCT4, SOX2, and NANOG (OSN) in mESCs from published datasets (F). Genes whose upstream or downstream DNA elements were described as ESC-specific super enhancers (H). “Corr” is the Pearson’s correlation coefficient.

(I) mRNA expression profile from normalized mRNA-Seq dataset from Tbx3^+/+ and Tbx3^N/N mESCs for the indicated gene sets. The expression data are represented as quantile scores, described in Supplemental Information. Significance calculated using Wilcoxon rank sum test with continuity correction.

(J) Protein levels of indicated ESC markers in mESCs cultured in presence of LIF.

(K) SSEA1-APC staining on mESCs grown in serum + LIF. IgM-APC stained cells used as negative control.