(A) Expression levels of Hox genes and of four housekeeping genes in both ES and E10.5 forebrain cells, as determined by RNA-seq. The large majority of Hox genes show low level activity in ES cells, whereas only few, very low, transcribed Hox genes are identified in E10.5 forebrain. In contrast, the expression levels of selected housekeeping genes are within a similar range (maximum threefold difference). (B) Overall gene expression patterns in ES and E10.5 forebrain cells are not significantly different. Box plots showing the overall distribution of RNA-seq signals per gene (RPKM), with colored boxes indicating the 25 to 75% range and whiskers indicating the 10 to 90% range. Differences between distributions were scored using a two-sided Welch two samples t test. (C) Quantitation of selected spliced Hox gene transcripts in ES cell and E10.5 forebrain samples as determined by RT-qPCR, with amounts in each sample relative to the Tubb2c gene. Below each sample, the specific product of a representative qPCR reaction is displayed. Color-coded dots are used to classify the different outcomes (see legend).