AP-2α and AP-2β cooperatively orchestrate homeobox gene expression during branchial arch patterning

RNA-seq of RNA isolated from E10.5 mandibular prominence of 3 control and 3 Tfap2a;Tfap2b;Wnt1CRE mutant mouse embryos. E10.5 mutant and litter-matched control embryos were dissected in ice-cold PBS. Subsequently, the mandibular prominences were carefully dissected from each embryo and stored in RNAlater (Ambion/Life Technologies) until later use. Following genotyping, RNA was extracted, essentially as previously described (Van Otterloo et al., 2016), from paired (i.e. left and right) mandibular prominences (3 control and 3 DCM embryos – 3 biological replicates) using the microRNA Purification Kit (Norgen Biotek Corp., Thorold, ON), following manufacturer's protocol. Following elution, mRNA was further purified using the Qiagen RNeasy Kit (Qiagen, Valencia, CA), according to manufacturer's protocol. Quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies, Santa Clara, CA) to ensure that it was of sufficient quality for library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). Following library generation and subsequent quality control assessment, cDNA was sequenced using the Illumina HiSeq2500 platform and single-end reads (1x150).