Figure 3

Global reorganization of the AC16 cell transcriptome in response to TNFα. GRO-seq in AC16 cells treated with a time course of TNFα reveals dramatic effect of signaling on the transcriptome. A) Pie chart showing the fraction of all transcripts expressed in AC16 cells that are regulated by TNFα at any treatment time point. B) Bar graph showing the fraction of all transcripts expressed in AC16 cells that are up- or downregulated in response to TNFα at the indicated time points. C) Heatmap representations of TNFα regulation of different classes of transcripts at the indicated time points. The transcripts in each class were clustered by their time-dependent expression levels using a hierarchical clustering algorithm. The color-based scale represents GRO-seq reads at the indicated time points scaled to the read density at time zero. In this representation, the x-axis (columns) is time of TNFα treatment and the y-axis (rows) is the individual transcripts. From top to bottom, the information has no particular order, although the clustering algorithm separates the distinct patterns of regulation. For example, those that are down regulated (blue) are at the top and those that are upregulated (yellow) are at the bottom.