RNASeq analysis of embryonic day 13.5 mouse cerebral cortex from (i) Pax6-deleted and (ii) Pax6- and Gsx2-deleted embryos

Mice carrying embryos that were either Pax6fl/fl Gsx2fl/+ Emx1CreER or Pax6fl/fl Gsx2fl/fl Emx1CreER were given tamoxifen on embryonic day 9.5 (E9.5) to induce either Pax6 deletion alone or Pax6 and Gsx2 deletion together. Embryos were harvested on E13.5, the cerebral cortices were removed and divided into rostral and caudal halves, and total RNA was extracted from the rostral half. Samples from littermates of the same genotype were pooled. Poly-A mRNA was purified and TruSeq RNA-Seq libraries were prepared and sequenced (100 base paired-end; Illumina, HiSeq v3).