Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA was extracted with Trizol using the RNAeasy Mini Kit (Qiagen, Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre, Inc.) with 5ug total RNA input. Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TruSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter, Inc.) and centered around 250 bp with the insert size ~130 bp. Second strand DNA was digested with Uracil-DNA Glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified. A total of 50 pools of 16 libraries were made, again randomly assigning samples to each pool. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of Illumina Hiseq2500 using 125 bp single-read v4 chemistry. Libraries with fewer than 5 million reads uniquely aligned to the D. melanogaster reference genome were re-sequenced to achieve sufficient read depth.