title: mRNA sequencing of PBCF cell line: NCI-PBCF-CRL-2336
design: TruSeq Stranded RNA Sample Preparation Kit was used to prepare cDNA libraries. The libraries were quantified with the Kapa kit and the Agilent 2100 Bioanalyzer.  Indexed libraries were loaded onto MiSeqTM flow cell to generate paired-end 2x50 bp reads.Pooled and validated libraries were run on HiSeq2000 (2x100 paired end runs).  The raw Illumina sequence reads converted to .fastq files and aligned to the reference genome (HG19/36) using TopHat.