Differential gene expression profiling in response to paraquat using a Drosophila Parkinson's disease model

Transcriptomic profiling using Drosophila heads reveals early gene expression responses to transient paraquat exposure. We performed RNAseq profiling of heads from the wild type (WT) Drosophila strain, Canton S (males only), that were fed either 2.5% sucrose (control) or 5 mM PQ in 2.5% sucrose for 12 h. Overall design: Transcriptomic profiling was performed using independent biological replicates per feeding. Age-matched adult Canton S male flies were fed either 2.5% sucrose (control) or 5 mM PQ in 2.5% sucrose for 12 h and the heads were collected for RNA extraction. For paired-end library preparation, NEBNext mRNA Library Prep Reagent Set for Illumina was used and the library concentration was analyzed by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Paired-end sequencing (25 million, 50-bp, paired-end reads) was performed using a 200 Cycle TruSeq SBS HS v4 Kit on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA) at the HudsonAlpha Institute for Biotechnology, Huntsville, AL. TopHat v2.0 were used to map raw reads to the reference Drosophila melanogaster genome dm3