GSE96871
Gene expression changes in the supraorbital cranial mesenchyme after beta-catenin deletion in vivo
Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at e13.5 cranial mesenchyme. Overall design: En1Cre;b-cateninfl/fl and En1Cre;b-cateninfl/+ supraorbital cranial mesenchyme was manually dissected from E13.5 embryos (4 mutants and 3 controls). RNA was isolated using Trizol and a Qiagen RNeasy Mini Kit. Libraries were prepared in the CWRU Genomics sequencing core using the Illumina TruSeq Stranded Total RNA kit-with Ribo Zero Gold. Paired-end sequencing was performed on an Illumina HiSeq 2500  v2 Rapid Run flowcell. The resulting 100bp reads were aligned to the mouse genome release mm9 genome using TopHat. Genomic assembly was completed using Cufflinks v1.3 (Roberts et al., 2011a, Roberts et al., 2011b, Trapnell et al., 2010, Trapnell et al., 2013). mm9_reFlat was used to annotate the data with a max intron length of 20,000 and genomic bias correction. Differential gene expression was determined with CuffDiff using the default settings plus genomic bias correction. contributor: Case Western Reserve University