Anaesthetized adults were placed in a 15ml conical tube, flash frozen in liquid nitrogen, then shaken vigorously for 10 seconds. Broken flies were placed on a Petri dish on dry ice and frozen severed heads were removed with forceps to a fresh tube. Flies were processed in groups of 100 animals per dissection. Typically, heads were missing the antennal and maxillary organs, while the mouth-parts were retained.

Total RNA was isolated using Trizol, then Qiagen RNeasy spin columns. mRNA was isolated using Dynal oligo(dT) beads, then fragmented using divalent cations under elevated temperature, followed by sequential ligation of RNA linkers to the 5’ and 3’ ends. Next, reverse transcription was performed using a primer complementary to the 3’ linker and PCR was performed using primers complementary to both linkers. ~ 300 bp fragments were isolated from an agarose gel and gel-purified again.

Reads were aligned to Dmel_Release_6 using the STAR aligner v2.3.0e (Linux x86_64) with default parameters on the FASTQ files to generate multiply-mapped BAM files. These were filtered to include reads with only 1 aligned hit ( NH:i:1 attribute) to generate uniquely-mapped BAM files. A custom script was used to convert BAM files into bedgraph files (bam2bedgraph.cc).