Differentially Expressed Genes in PPARγ-deficient MSCs

Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulator of adipogenesis. It is also a central player in energy metabolism, inflammation and immunity. As an important nuclear transcription factor, PPARγ can regulate the expression and function of genes or biological processes directly or indirectly via association with other factors and modulate their activities. To exploit the impact of PPARγ on global gene expression profile, we report in this study the bioinformatics data analysis results revealing the changes of genes and pathways in the absence of PPARγ. In brief, we performed RNA deep sequencing (RNA-Seq) analysis using RNA samples isolated from multipotent mesenchymal stromal cells (MSCs) of PPARγ knockout and wild type control mice. The RNA-Seq data sets were then subjected to bioinformatics analyses from different angles to reveal the scale and depth of PPARγ in different biological processes. Our results not only recapitulated the known functions of PPARγ, it also revealed new genes and networks influenced by PPARγ and shed new lights on our current understanding of this nuclear receptor in health and disease. microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Expression profile of genes in PPARγ-deficient and PPARg-floxed MSCs were analyzed by RNA-Seq on a HiSeq2000 sequencing machine.