title: D. melanogaster Zhr x Z30 (MZ) paired RNAseq
design: 10 ug of total RNA from each sample was treated with DNAse 1 (Invitrogen) followed by poly(A)  selection using Dynal magnetic beads (Invitrogen) following manufacturer recommendations. Poly(A)  RNA was then fragmented using RNA fragmentation reagent (Ambion) before cDNA synthesis. Double-stranded cDNA was primed using random hexamers and Superscript II reverse transcriptase (Invitrogen). cDNA was run on a 2% agarose gel and the region corresponding to ~300bp fragments was gel extracted. This size-selected double-stranded cDNA was used in the Paired-End Genomic DNA Library Preparation Kit (Illumina) according to manufacturer’s recommendations.