Figure 3.

Differential RNA-seq analysis of mouse intracisternal A-particle and long interspersed element-1 in DNA methylation mutants. (a) Left: IAP fold-change (x-axis) plotted against probability density function (y-axis) in indicated cell types. Right: non-IAP LTR fold-change plotted against probability density function in indicated cell types. (b) Left: 10 kb upstream IAP fold-change plotted against probability density function in indicated cell types. Right: 10 kb upstream non-IAP fold-change plotted against probability density function in indicated cell types. (c) LINE-1 fold-change plotted against probability density function in Lsh−/− fibroblasts. (d) LINE-1 fold-change plotted against probability density function in Dnmt1−/− fibroblasts. (e) LINE-1 fold-change plotted against probability density function in TKO ES cells. (f) LINE-1 fold-change plotted against probability density function in E13.5 embryos. Vertical lines indicate −5 and +5 log2-fold changes. X-axis is log2-fold change in repeat RNA expression; y-axis is probability density function (P.D.F.). fib, fibroblasts; TKO ESC, triple knockout embryonic stem cells.

Dunican et al. Genome Biology 2013 14:R146   doi:10.1186/gb-2013-14-12-r146
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