RNA-seq analysis of Wnt1-Cre;Rosa26-Dlx2 mouse

Total RNA was extracted using Trizol from freshly dissected E10.5 maxillary process tissues. Three independent RNA samples were prepared for each genotype (WT and wnt1^cre; Rosa26^Dlx2/-). We used 2 μg total RNA as input material for the library preparations for each sample. Sequencing libraries were generated using the NEBNext^® UltraTM RNA Library Prep Kit for Illumina^® (#E7530L, NEB, United States) following the manufacturer’s recommendations. The libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated. Sequenced reads were mapped to the mm 10 genome using STAR aligner version 2.7.3a. Comparisons between the RNA-seq datasets were performed using the DESeq2 package in R. Enrichment analyses and visualization of functional profiles of differentially expressed genes (DEGs) were performed using the clusterProfiler package in R.