Next generation sequencing analysis of primary rat lung fibroblast, primary rat lung alveolar type 2 cell and a novel 10-4A rat lung cell line transcriptomes

Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of a novel 10-4A rat lung fibroblast cell line and compared the transcriptome to freshly isolated primary rat lung fibroblasts and freshly isolated primary rat lung alveolar type 2 cells. Overall design: Methods: mRNA profiles 10-4A, primary fibroblasts and primary alvelar type 2 cells 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.