4.5. RNA Sequencing and Transcriptome Data Analysis

TruSeqTM RNA Sample prep kits (Illumina, San Diego, CA, USA) were used to prepare the RNA-Seq transcriptome libraries from total RNA according to the manufacturer’s protocol [33]. Next, the library was sequenced with an Illumina HiSeq 2000plat form (Macrogen Corporation, Seoul, Korea). To check quality of RNA sequencing data, SolexaQA software [34] was used to investigate base quality scores from FASTQ files generated by Illumina sequencing technology. The reads from the FASTQ files were mapped against the human reference genome using TopHat version 2.0.6 (http://tophat.cbcb.umd.edu/). Transcripts with a fold change ≥ |2.0| and p-value < 0.05 were considered statistically significant and were included in downstream analysis.