title: Murine Cytomegalovirus infection of Balb/c murine embryo fibroblasts Transcriptome and Gene expression
design: Next generation sequencing – library preparation, alignment and analysis. Total RNA was extracted from Balb/c MEF cells cultured in 100mm2 petri dishes and exposed to 0.3 PFU/cell of the MW 97.01 strain of murine cytomegalovirus or mock-infected. At 4, 8, 12, 16, 24, 32, 40, 60 and 80 hours after infection, RNA was isolated using TRIZOL Reagent. RNA integrity was assessed on Agilent Bioanalyzer and only samples with RNA index values of at least 9 were used. Equal amounts of RNA from each time point were pooled (0.3 ug of RNA per time point) and treated with DNaseI. Libraries were prepared with Illumina TruSeq RNA kit according to manufacturer’s instructions and sequenced on Illumina Genome Analyzer IIx as single-end 36 bp reads.  The Illumina TruSeq RNA kit employed does not allow for strand-specific information to be derived from the sequence data. Reads were aligned to mouse (NCBI37/mm9 assembly) and MCMV genome (GenBank acc.no. NC_004065.1) using ELAND aligner