Computational protocol: Rational Design of a Live Attenuated Dengue Vaccine: 2′-O-Methyltransferase Mutants Are Highly Attenuated and Immunogenic in Mice and Macaques

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Protocol publication

[…] Virus was isolated from mouse serum with Qiagen Viral RNA extraction Kit.Fifty ng of viral RNA were used to prepare cDNA libraries using the Illumina TruSeq RNA sample preparation kit according to manufacturer's protocol. The only protocol modification was the removal of the mRNA enrichment step. The cDNA libraries were sequenced as a multiplex in a single lane of an Illumina HiSeq2000 (Next Generation Sequencing Core facility, Genomic Institute of Singapore). One to 2 million 50 bp paired-end reads were generated for each virus.Wild-type and mutant virus samples were mapped to their respective reference genomes using Bowtie 2 . Mapping statistics and genotype calls were made with SAMtools . Data analysis was performed in Pipeline Pilot (http://www.accelrys.com). At least two reads with an alternate base at a given position were defined as a SNP. […]

Pipeline specifications

Software tools Bowtie, SAMtools
Application WES analysis
Organisms Mus musculus, Macaca mulatta, Homo sapiens
Diseases HIV Infections