UR domains have low gene content and expression both in vivo and in vitro.

A. In vitro TGCs produce the same UR domains as in vivo. 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 (in vivo); blue: day 3 (in vitro); green: day 5 (in vitro); orange: day 7 (in vitro). Two biological replicates are plotted for each cell type. Dashed line: FDR = 0.0001. All autosomes shown in Figure S8. B. Location of UR domains on the autosomes of cultured TGCs compared to e9.5 in vivo 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 in vivo 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. C. 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. D. Low gene expression in UR domains in vivo. Plot of TGC normalized expression (NE) counts versus level of representation (NLog2 of e9.5 TGCs vs. embryos (WGS)). UR domains boxed in pink. E. Low gene expression in UR domains in vitro. 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.