Total RNA from Teladorsagia circumcincta was converted to double                 stranded cDNA by CLONTECH SMARTerTM cDNA construction kit. First strand cDNA was                 synthesised using PowerScriptTM Reverse Transcriptase (RT) from a modified 3'-primer                 with oligo(dT) sequence (CDS III/3' PCR Primer) that annealed to the poly-A stretch                 of RNA and synthesised cDNA until the 5' end of the mRNA. Finally, double stranded                 cDNA synthesis was performed using PCR amplification, and the final product contains                 the CLONTECH SMART IV Oligo and CDS primer at 3' and 5' ends. The cDNA was                 fragmented, size-selected, library-prepped, and sequenced according to standard                 Roche-454 Titanium protocols. The only variation from the method manuals is in the                 Library prep as we use the Covaris S2 for DNA shearing not a Nebulizer as outlined                 (The covaris settings were for 500bp peaks).