Next Generation Sequencing Analysis of primary rat lung fibroblast transcriptomes

Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of primary rat lung fibroblast cultured on 3-5 kPa PDMS compared to plastic over a 14-day timecourse. Overall design: Methods: mRNA of primary fibroblasts were generated by deep sequencing, in triplicates or quadruplicates, using Illumina HiSeq2000. Sequenced read quality was checked with FastQC v0.11.2. Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment. The gene expression profiles were quantified using Cufflinks software version 2.2.