Degree of underrepresentation varies over developmental time.

<p><b>A</b>. UR domains exist at e8.0 and further develop over time. Plot comparing position along chromosome 14 to the NLog2 Ratio of sequence coverage of TGCs vs. embryos. Red: e9.5; blue: e8.0. Two biological replicates are plotted for each stage (LitterA shown for WGS). Dashed line: cut-off for significance. All autosomes shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004290#pgen.1004290.s006" target="_blank">Figure S6</a>. <b>B</b>. e8.0 TGCs have a subset of the UR domains found at e9.5. Venn diagram showing overlap of UR domains between both e8.0 replicates (one litter each) and UR domains common to all six e9.5 individuals. Asterisk represents the one UR domain present in both e8.0 replicates that is present in only 5/6 of the e9.5 individuals. <b>C</b>. Size and depletion of UR domains increases between e8.0 and e9.5. “e8.0 all”: UR domains present in both e8.0 replicates; “e8.0 shared”: UR domains present at e8.0 that are also present at e9.5; “e9.5 all”: all UR domains present in all six e9.5 individuals; “e9.5 shared”: UR domains present at e9.5 that are also present at e8.0. Box plot on left compares these classes of UR domains to size (0–8,500 kb), while box plot on right compares these classes to percent median depletion (15–60%). Asterisks mark comparisons that are statistically significant (p<0.01). <b>D</b>. UR domains present at late gestation. Plot comparing position along chromosome 14 to the NLog2 Ratio of array intensity of TGC vs. embryo. Red: e9.5; blue: e11.5; green: e13.5; orange: e16.5. Two biological replicates are plotted for each stage. Dashed line: FDR = 0.0001. All autosomes shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004290#pgen.1004290.s007" target="_blank">Figure S7</a>. <b>E</b>. Location of UR domains during the second half of gestation. Summary of results from both biological replicates of aCGH of TGCs from e9.5, e11.5, e13.5, and e16.5, all versus embryos (FDR = 0.0001). Darker green/longer bars indicate UR domains present in more replicates. Asterisks indicate the location of UR domains present at e9.5. <b>F</b>. Depletion of UR domains does not significantly change between e9.5 and e16.5, however, depletion of UR domains significantly differs between biological replicates at e13.5 and e16.5. Box plot compares percent median depletion of each biological replicate at stages e9.5, e11.5, e13.5, and e16.5. To compare with (<b>C</b>), aCGH data was normalized to WGS depletion levels (e9.5). Asterisks mark comparisons that are statistically significant (p<0.01).</p>