A.Catalan, S.Hutter, J.Parsch, Population and sex differences in Drosophila melanogaster brain gene expression,, (BMC Genomics 13: 654, 2012).

The authors used RNA-seq (Illumina platform, 50-base single-end reads) to analyze the transcriptomes of dissected brains of males and females (4-6 days old). Flies from two populations (The Netherlands and Zimbabwe) were used. There were two biological replicates of each population and sex.

The text is freely available at:
http://www.biomedcentral.com/1471-2164/13/654

Raw RNA-seq data are available under the GEO series GSE40907:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40907

For Sebida, we performed an updated statistical analysis of the Catalan et al. short-read data, using NextGenMap and DESeq2, as described in:

A.K.Huylmans, J.Parsch, Variation in the X:autosome distribution of male-biased genes among Drosophila melanogaster tissues and Its relationship with dosage compensation,, (Genome Biol. Evol. 7: 1960-1971, 2015).
http://gbe.oxfordjournals.org/content/7/7/1960.long
The M/F ratios are for the combined analysis of both populations. The FDR values represent the Benjami-Hochberg corrected P-values from DESeq2.