The violin plot of fig. S3C shows the pausing of polymerase II for the genes present in the different categories defined on the heatmap of fig. S3A. The pausing index was calculated as being the ratio of the mean values at TSS - 300 bp + 100 bp and 50% of gene body to transcription end site (TES). The number of genes for the different categories in fig. S3A (top to bottom) is as follows: 3159, 1492, 487, 2002, 4288, and 2013, respectively.

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