Fig. 3

Depletion of FACT disrupts transcription of pluripotency factors. A Volcano plot of differential mRNA transcription after 24-h treatment (TT-seq, analyzed with DESeq2). Red points indicate significant changes (adj. p < 0.05, |log₂ fold change|> 0.75). Light blue points are significant changes by adjusted p-value but below the fold change cutoff, while dark blue points are significant changes by log₂ fold change but below the adjusted p-value cutoff (for plotting, adj. p < 10⁻⁶). B Volcano plot of differential mRNA abundance after 24-h treatment (traditional RNA-seq, analyzed with DESeq2). Points are colored as in panel A. C IGV genome browser tracks showing nascent transcription (TT-seq) from the Nanog gene following 24-h IAA treatment to deplete SPT16. Averaged replicates are shown as a single track, oriented to the genic strand (n = 3). D As in B but visualized over the Sox2 gene locus. E DESeq2 results: mRNA transcription of seven pluripotency factors across depletion timecourse. Significance of altered pluripotency factor transcription was analyzed by Friedman tests and corrected for multiple comparisons via Dunn’s test (p = 0.0027). F Pathway analysis of differentially expressed genes following 24-h IAA treatment to deplete SPT16. Y-axis indicates enrichment ranking. Q-values were calculated from p-values by the Benjamini–Hochberg procedure