Profiling of Stem/Progenitor Cell Regulatory Genes of the Synovial Joint by Genome-wide RNASeq Analysis

We report the application of RNA sequencing technology for high-throughput profiling of the articular and mature zones of the mandibular condyle in postnatal 7-day-old mice. Briefly, mandibular condyles of postnatal 7-day-old mice were frozen-sectioned with articular, mature zones idintified under a dissection microscope. Cells from the articular zone (az), mature zone (mz) were isolated by laser capture microscopy. Total RNAs from each sample were polyA selected and single-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit (Illumina). The samples were then sequenced using the Illumina HiSeq sequencer. Total sequencing reads representing RNA transcripts were generated and were mapped to the NCBI mouse reference genome. Differential expressed genes were identified using DESeq, with <0.05 false discovery rate (FDR). Fragments Per Kilobase of exon model per Million Mapped fragments (FPKM) were estimated for each gene in each sample. Hierarchical clustering was also performed on log2FPKM values with Cluster 3.0. Only genes with FDR<0.05 and =0.80 standard deviation were included. RNA comparison between articular and mature zones revealed distinctive gene expression profiles. Overall design: Profiling of the articular and mature zones of postnatal 7-day-old mice mandibular condyle by RNA sequencing, in triplicate, using Illumina HiSeq sequencer.