Lineage-specific enriched and depleted genes revealed distinct differentiation programs.

<p>(A) Graphs of the number of genes specific to each lineage. The gene lists and permutation tests are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002575#pgen.1002575.s002" target="_blank">Dataset S2</a>. The “♂” and “♀” symbols indicate lineage-specific and sex-specific genes, while the “♂+♀” symbol indicates genes that are lineage-specific and sex-independent. Pale bars below the axis indicate genes that are depleted relative to other lineages. The E11.5 graphs are on the top row, the E12.5 graphs are in the middle, and the E13.5 graphs are on the bottom row. The germ cell Y-axis is scaled to accommodate the larger number of genes specific to this lineage. Leydig cell genes (burgundy) were separately identified by cross-referencing the endothelial and interstitial data and added to the bars for the XY interstitium. Lists with >20% false positives are indicated by “ns”. Lists with no genes are marked with “0”. Some bars also have a colored gene name exemplifying the pattern within that category (the graphs for <i>Dhh</i> and <i>Flt1</i> appear in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002575#pgen-1002575-g001" target="_blank">Figure 1B</a>). (B) Graphs of the log-transformed, normalized intensity values for genes that are sex-specifically (<i>Ccna2</i>) and sex-independently (<i>Gata6</i>) depleted. The error bars are standard error. Three lineages showed specific gene depletion in addition to enrichment. Each lineage had transcriptionally distinct progenitors as indicated by “♂+♀” genes at E11.5. Supporting cells were already in the midst of their sex-specific differentiation by E11.5 as indicated by genes in the “♂” or “♀” columns at E11.5, but the other cell types were sexually undifferentiated at E11.5.