RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human mesenchymal stem cells differentiation from human embryonic stem cells and adult bone marrow mesenchymal stem cells

Purpose: The goals of this study are to identify the process and the key transcription factors and signaling pathways governing differentiation through comparing the transcriptome profilings in hESC samples collected from day 0 to day 7 after mesenchymal stem cells differentiation with human adult bone marrow MSCs. Methods: mRNA profiles of human adult bone marrow MSCs and hESC samples collected from day 0 to day 7 after mesenchymal stem cells differentiation were generated by deep sequencing using Illumina GAIIx. 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 TaqMan and SYBR Green assays Conclusions: Our study represents the first detailed analysis of mesenchymal stem cells transcriptomes from human embryonic stem cells, generated by RNA-seq technology. We provide a framework for comparative investigations of expression profiles and help illustrate the key signaling and transcription factors during hESCs differentiation towards MSCs. 7 samples