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PCR products were gel purified, cloned and sequenced on an ABI 3100 sequencer (Applied Biosystems) using standard cycle sequencing protocols.
All amplicons were sequenced on a 454 Genome Sequencer FLX System (Roche Diagnostics GmbH) following amplicon sequencing protocols (http://www.454.com).
This chapter outlines the sequencing protocols for the detection of human genome variation.
Libraries were sequenced on Illumina GAIIx, generating 38- and 90-base paired end (PE) reads, for the first and second sequencing protocols, respectively.
The standard library amplification step in most sequencing protocols substitutes erroneous bases for the ones that have been modified, yielding high-quality but incorrect sequences.
Formalin-fixed and paraffin-embedded tissue has not been used in large-scale sequencing protocols.
For each taxa set, we used the PCR and sequencing protocols described above.
We followed the sequencing protocols used by Álvarez-Iglesias Álvarez-Iglesiasch aretbriefly described here.
The library was sequenced on Illumina GA sequencing instrument according to standard Illumina cluster generation and sequencing protocols.
PCR primer pairs spanning contig regions, which contained putative SNPs between the individual fish, were used to amplify and sequence genomic DNA using standard Sanger sequencing protocols.
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This study points to a need for more rigorous pre-sequencing protocols and laboratory standards.
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