GSM5970652: mutant_RNAseq_Rep1; Mus musculus; RNA-Seq
RNA-sequencing:   For RNA-sequencing E10.5 facial prominences encompassing ectoderm and mesenchyme of the mandibular, maxillary, and nasal prominences were micro-dissected in ice cold PBS using insulin syringes and stored in RNA-later at -20°C.  Once sufficient EDKO (Crect; Tfap2aflox/null; Tfap2bflox/null) and control littermate samples lacking Crect (e.g. Tfap2aflox/+; Tfap2bflox/+) were identified for 3 biological replicates of each, tissue was removed from RNA-later and RNA harvested as previously described using the microRNA Purification Kit (Norgen Biotek) and following manufacturer's protocol (Van Otterloo et al., 2018).  Following elution, mRNA was further purified using the Qiagen RNAeasy Kit according to the manufacturer's protocol. The quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies) prior to library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit. All libraries passed quality control guidelines and were then sequenced using the Illumina HiSeq2500 platform and single-end reads (1×150) to a depth of ~15-25x106 reads per sample. To identify differentially expressed genes between control and mutant groups, we next utilized a standard bioinformatic pipeline for read filtering, mapping, gene expression quantification, and differential expression between groups (see below). Library construction and sequencing was carried out by the University of Colorado, Anschutz Medical Campus, Genomics and Microarray Core.