Fig. 2: SOX2 dynamics configure the WNT response of epiblast-like cells.
a, Sox2-OFF cultured in FLC medium exhibit altered expression of CEpiLC-specific genes. Genes shown are upregulated in CEpiLC compared with EpiLC (log2 fold change (log2FC) >1, false discovery rate (FDR) <0.05). FDR was determined by DESeq2 padj metric from n = 3 biological replicates. k-Means clustering (k = 3). Illustrative genes for each cluster are highlighted. b, Genes upregulated in SOX2-OFF compared with CEpiLCs include early/anterior streak and mesendoderm markers. Genes shown are differentially expressed (log2FC >1, FDR <0.05) in a comparison between SOX2-OFF and CEpiLC. FDR was determined by DESeq2 padj metric from n = 3 biological replicates. k-Means clustering (k = 2). Illustrative genes for each cluster are highlighted. c, SOX2-ON cultured in FLC medium express low levels of EpiLC- and CEpiLC-specific genes. Genes shown are differentially expressed (mod(log2FC) >1, FDR <0.05) in a comparison between EpiLCs and CEpiLC. FDR was determined by DESeq2 padj metric from n = 3 biological replicates. k-Means clustering (k = 3). Illustrative genes for each cluster are highlighted. d, SOX2-ON express elevated levels of pluripotency-associated genes compared with CEpiLCs and EpiLCs. Genes shown are differentially expressed (log2FC >1, FDR <0.05) in a comparison between SOX2-ON and CEpiLCs. FDR was determined by DESeq2 padj metric from n = 3 biological replicates. k-Means clustering (k = 3). Illustrative genes for each cluster are highlighted. e–g, Measurement of relative mRNA expression by RT–qPCR shows that expression of the pluripotency factor Nr5a2 is reduced (e), the neural marker Sox1 increases (f) and the posterior marker Hoxb9 is not expressed (g) when SOX2-ON are transferred from FLC to FL medium. SC, spinal cord. Each datapoint represents an individual biological replicate. Bars denote mean ± s.e.m. P values calculated for differences of mean expression by two-tailed Student’s t-test are shown. In e, n = 6 ‘LC’ and n = 4 ‘L’ samples; in f, n = 6 ‘LC’ and n = 8 ‘L’ samples; and in g, n = 6 ‘LC’ and n = 4 ‘L’ samples. mod, absolute value. Source numerical data are available in source data.
