Control DNA sequences for analysis of allelic imbalance in D. melanogaster - D. simulans hybrid head tissues
Approximately 1 µg of gDNA was fragmented (standard probe sonicator, Duty Cycle 80%, Output 2, sets of 20 pulses for 5 rounds) and concentrated using the Zymo Research DNA Concentrator kit (10 µl). Libraries were constructed using reagents from the End-IT Repair kit (Epicentre), Fast-Link DNA Ligation Kit (Epicenter), Illumina Genomic DNA Sample Prep Kit (part # 1000181), addition of an A base (Klenow 3´?5´ exo–, NEB) and Zymo Research DNA Concentrator kits. In brief, samples were processed to produce 5´-phosphorylated, blunt-ended DNA followed by A overhang addition. Illumina genomic DNA adaptors (2 µl adaptor oligo mix 10 mM) were  ligated to DNA fragments and processed DNA was size selected (200-500 bp) by gel purification. Cleaned, concentrated, size selected templates were PCR enriched for adaptor modified cDNA following the Illumina Genomic DNA Sample Prep protocol.