Figure 1.

Naive and Primed Human ESCs Exhibit Strong Differences in Gene Expression

(A) Naive and primed human ESCs were cultured in N2B27 supplemented with t2iL+Gö or in E8 medium, dissociated into single cells, and sorted into 96-well plates loaded with RLT lysis buffer and External RNA Controls Consortium (ERCC) spike-ins. RNA-seq libraries were prepared using the SmartSeq2 protocol and submitted for sequencing.

(B) PCA plot of hESC expression profiles, constructed from batch-corrected and normalized log expression values of highly variable genes detected across the entire dataset. Cells are colored by their condition, and the percentage of variance explained by the first two principal components is shown.

(C) Smear plot of log₂-fold changes in expression between the naive and primed conditions, where differential expression (DE) genes were detected using edgeR at a false discovery rate (FDR) of 5%.

See also Figure S1 and Table S1.