RNAseq Dmel, F1 crosses between DGRP lines: 808M x 208F mh R1
We obtained sex-specific replicated gene expression for heads and gonads from crosses within- and between Drosophila melanogaster inbred lines. Specifically, we randomly selected 6 lines from the Drosophila Genetic Reference Panel (DGRP, Mackay et al. 2012) without Wolbachia infection and main inversions (Huang et al. 2014) and matched them into three pairs: DGRP-757 x DGRP-392, DGRP-208 x DGRP-808 and DGRP-83 x DGRP-332. Crosses within and between lines were set up in vials containing 40 males and 40 virgin females (between 1 and 5 vials depending on the number of individuals that could be obtained), at 23oC under a 12 hours light / 12 hours dark cycle. For each cross, we then dissected two replicate samples of heads and gonads of 20 4-day-old virgin females and virgin males for each within-line and reciprocal between-line cross, obtaining a total of 96 samples (experimental design outlined in Figure S1). Samples were flash frozen in liquid nitrogen and kept at -80oC until further processing. RNA was then extracted with a Maxwell RSC Simply RNA Tissue  Kit (Promega). Two Smart-seq2 RNA-seq libraries were produced from the tagged and pooled samples at the Vienna Biocenter Sequencing Facility (one for each replicate), and sequenced on an Illumina Novaseq machine (single end 100bp reads). The data is single-read. The reverse read files contain UMI information (to be used for deduplication).