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Second, for each gene PCR amplification was performed with equal amounts of purified fragments #1 and #2 as templates and with no additional primers, yielding the fusion genes mamK-venus and mamK-like-venus.
Libraries were sequenced using two methods: with Roche 454 Titanium on pooled RNA from all 14 tissues to generate long reads to serve as alignment templates; and with the Illumina Genome Analyzer to generate high sequence coverage and transcript counts (for use in analyses to be published separately).
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Control reactions were conducted with no cDNA template and with RNA to determine the level of background or genomic contamination.
Each model was aligned both with its respective template and with a fourth template that also fits the LeuT/vSGLT/Mhp1 fold (BetP).
The individual fluorescent proteins were amplified by PCR with pmTFP1 or mVenus as a template and with the following two primers 5′-GATCAGTACTAATGGTGAGCAAGGGCGAG and 5′-TGATCGCGGCCGCTCTTGTACAGCTCGTCCATGC.
The mTFP1-5aa-Venus gene was amplified by PCR with pmTFP1-5aa-Venus as a template and with the following primers: 5′-CGCTACCGGTCGCCACCA and 5′-GATCGCGGCCGCTTAGTACCGTCGACTGCAGAATTC.
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