Study Protocol Description A liver fluke was collected from a sheep from an abattoir in north Wales. Refer to manuscript for more information. SMART cDNA synthesis and amplification (Zhu et al., 2001) was followed by Duplex-Specific Nuclease (DSN) normalisation. 80ng of this normalised sample was subjected to a further round of amplification using the Advantage 2 Polymerase mix and 0.4 microM SMART PCR primer (Clontech Laboratories, France) following the manufacturer's instructions. The resulting product was purified using QIAquick PCR purification columns (Qiagen, Crawley, UK) to a final concentration of ~300 ng/ microliter prior to pyrosequencing sequencing.  At least 4 microgram of normalised cDNA was submitted to the Advanced Genomics Facility (AGF) at The University of Liverpool where the sample was prepared using methods essentially as those described by Margulies et al., 2005:  sample quality was first assessed using the Agilent bioanalyser and then the sample was nebulised into 300-500 bp fragments, blunted and ligated to short adapters. Each fragment was then fixed to DNA capture beads (one fragment one bead) and subjected to emulsion PCR (emPCR).  All fragments were amplified in parallel and then placed into individual wells of a PicoTiterPlate where they were sequenced also in parallel using the Genome Sequencer FLX Instrument (Roche). DSN normalisation is described in Zhulidov et al, 2004 and enriches for full length transcript sequences and equal transcript abundance. Refer to manuscript.