RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

Purpose: The goals of this study are to determine possible downstream targets of Twist1 in bone marrow stromal cells with or without Twist1 knockout. Methods: gene expression profiling with or without Twist1 knockout in bone marrow stromal cells were generated by deep sequencing, using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Conclusions: Notch signaling were activated after Twist1 knockout. Overall design: mRNA profiles of stromal cells with or without Twist1 knockout were generated by deep sequencing using Illumina Hiseq.