title: RNA-Seq of Homo sapiens: LCLs after ionizing radiation
design: Total RNA was extracted using RNeasy micro-kit (QIAGEN) from 10 lymphoblastoid cell lines in three conditions (no irradiation, and two post irradiation, and six hours post irradiation). cDNA was synthesized using random hexamer primers by TaqMan Reverse Transcription Reagent kit (Applied Biosystems). RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep kit (Illumina, #20020596) and sequenced on HiSeq 2500. An average of 60 million unique 100-nt reads per sample was generated. Sequencing reads were preprocessed to remove adapter sequences from the end of reads using the program fastx_clipper from FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Low-quality sequences at the ends of reads represented by stretches of # in the quality score string in FASTQ file were also removed. Reads shorter than 35 nt after trimming were excluded from analysis. Sequencing reads were aligned tohuman reference (hg18) using GSNAP (version 2013-10-28) (59) using the following parameters: mismatches % [(read length + 2)/12-2]; mapping score R 20; soft-clipping on (-trim-mismatch-score=-3). Read counts from each sample were normalized to the total number of mapped reads.