Additional file 6: Figure S4.

Density scatter plots of normalized read counts for protein-coding genes and surrounding regions. Read counts from experiments in which embryonic stem cell (ESCs) were nucleofected with antisense oligonucleotides (ASOs) targeting the 5′ and 3′ parts of 7SK (y-axis) were plotted versus counts for ESCs nucleofected with scrambled control ASOs (x-axis), to illustrate the overall change in expression levels after 7SK depletion. Color intensity indicates the density of data points. Note the increased read coverage in upstream and downstream regions in 7SK-depleted samples. Read counts were normalized by the trimmed mean of M-values (TMM) algorithm (see Materials and Methods) and incremented by a pseudocount of 1 to enable visualization on a logarithmic scale. Upstream and downstream 5 kb regions were selected as described in Materials and Methods to avoid inclusion of segments from neighboring genes.

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Castelo-Branco et al. Genome Biology 2013 14:R98   doi:10.1186/gb-2013-14-9-r98