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The old Illumina ligation conditions changed with the TruSeq kit. I had trouble swapping in TruSeq adapters for the old adapters using the old protocol, and I don't know why. Does anybody happen to know why, and by chance which ligase they're using now?
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Hi jlove,
Could you be a bit more specific? The conditions changed from which kit to which other kit? (Cat numbers, if possible).
Very unlikely they switched ligases. For double-stranded DNA, T4 DNA ligase is nearly universally used.
If you mean you tried to swap in TruSeq Adapters for the adapters used in the Paired-End Sample Prep kit (PE ‐ 102‐ 1001/PE ‐ 102‐ 1002), then it may be that you would also need to use the TruSeq PCR primers for the enrichment PCR step.
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Phillip
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