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. 2014 Jul 24;10(7):e1004483. doi: 10.1371/journal.pgen.1004483

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© 2014 Gyenis et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Pol II reads were calculated around the TSS (+/−300 bp), on the gene body (−100 bp from TSS until EAG) and downstream from EAG (from EAG to EAG +4 kb) for well characterized DNA repair and UV responsive genes (from the KEGG database) from each ChIP-seq dataset. From the collected values heat map was generated, and genes are organized into groups based on similar Pol II behavior by using k-means clustering. Pol II occupancy changes are represented as in Figure 4. Red color shows increased; green color shows decreased Pol II tag numbers in percentages compared to data obtained from the control non-UV irradiated cells (black color). Black color also refers to no change in Pol II density. The figure is labeled similarly as Figure 4.