UR domains have low gene content and expression both <i>in vivo</i> and <i>in vitro</i>.

<p><b>A</b>. <i>In vitro</i> TGCs produce the same UR domains as <i>in vivo</i>. Plot comparing position along chromosome 14 to the NLog2 Ratio of array intensity of TGC vs. embryo (e9.5) and TGC vs. TS cells (day 3, 5, and 7). Red: e9.5 (<i>in vivo</i>); blue: day 3 (<i>in vitro</i>); green: day 5 (<i>in vitro</i>); orange: day 7 (<i>in vitro</i>). Two biological replicates are plotted for each cell type. 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.s008" target="_blank">Figure S8</a>. <b>B</b>. Location of UR domains on the autosomes of cultured TGCs compared to e9.5 <i>in vivo</i> TGCs. Summary of results from both biological replicates of aCGH of cultured TGCs differentiated 3, 5 and 7 days vs. TS cells, and of e9.5 <i>in vivo</i> TGCs vs. embryo (FDR = 0.0001). Darker green/longer bars indicate UR domains present in more replicates. Asterisks indicate the location of UR domains present in both replicates at e9.5. <b>C</b>. UR domains are gene poor. Histogram plotting number of Ensembl genes versus level of representation (NLog2 of TGCs vs. embryos (WGS)). UR domains boxed in pink. <b>D</b>. Low gene expression in UR domains <i>in vivo</i>. Plot of TGC normalized expression (NE) counts versus level of representation (NLog2 of e9.5 TGCs vs. embryos (WGS)). UR domains boxed in pink. <b>E</b>. Low gene expression in UR domains <i>in vitro</i>. Plot of TGC NE counts versus level of representation (NLog2 of day 7 TGCs vs. TS cells (aCGH)). Genes not present on the array were filtered out. UR domains boxed in pink.</p>