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Oligonucleotide primers were designed using a primer design centre (http://www.probelibrary.com/) and synthesized by Invitrogen (Stockholm, Sweden).
Primers were designed for CDH8, PCDH10, DNMT1, DNMT3a and DNMT3b using a primer design tool (Integrated DNA Technologies, Coralville, IA, USA).
We selected SNPs located at least 750 bases away from a sequence contig gap (to make primer design feasible) reducing the number of testable SNPs to 393 of which 348 yielded primers using a primer design package[ 13].
Oligonucleotide primer pairs for thyroid hormone-β receptor (Thrb) glutathione reductase (Gsr) were designed using a primer design program (Primer Express, Applied Biosystems) and obtained from Integrated DNA Technologies Coralvillee, IA).
Both primer panels were devised using a primer design algorithm described in detail by Komori et al. The primer design pipeline utilizes the Primer3 software as well as electronic PCR to restrict off-target amplification.
Genomic primers for Polymerase Chain Reaction (PCR) amplifications of the entire coding region and intron exon boundaries of SORT1, LAPTM5 exon 5, and GRIN2D exon 13 were designed using a primer design public website (http://ihg.gsf.de/ihg/ExonPrimer.html; primer sequences available upon request).
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A nested PCR assay was developed for the specific amplification of parasite DNA, using a primer designed to span the exon intron boundary.
A complete cDNA fragment encoding this putative caleosin was obtained by PCR cloning using a primer designed according to the tryptic peptide and another one designed according to a highly conservative region among diverse caleosins.
To clone the 5' parts of the S4 segment, cDNA was synthesized using a primer designed from the partial sequence obtained above, as described previously [ 47].
Because EcR is a 20E-inducible gene, we first examined the overall level of induction of EcR by qRT-PCR using a primer designed against the 3' region of the gene common to all isoforms.
As the only biological material available was from the sister species T. cati, PCR was carried out using a primer designed to the 5' end of the T. canis hsp-90 sequence (5'-ATGTCCGAGTTTCAACAACAACCAG-3') together with the degenerate 3' primer described previously (see above) on cDNA extracted from adult T. cati worms.
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