title: helianthus_hybrid_species_transcriptome
design: For each individual, we extracted RNA using a modified TRIzol Reagent protocol (Invitrogen, Carlsbad, CA, USA). We quantified the RNA samples using a NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and verified their quality on agarose gels. We stored the total RNA in pure water. Libraries were then prepared following standard Illumina Tru-Seq (LT) Protocol (pp 35-69) with one slight modification. The RNA was not fragmented during the poly-A mRNA purification step, but directly reverse transcribed into cDNA. Upon cDNA purification, samples were then sheared to ~ 400 bp on a Covaris (Woburn, MS, USA) sonicator. These were then sequenced on either the Illumina GAIIx or Illumina HiSeq 2000 platform (paired end sequencing, 2 X 100bp). Base calling was performed via the standard Illumina casava (1.8) pipeline.