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Old 05-25-2015, 06:53 AM   #12
pmiguel
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
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Quote:
Originally Posted by nucacidhunter View Post
They offer two transposase based kits one for SureSelect QXT capture and another for WGS library prep. There is no info in manuals on transposase used, but for sequencing one must use custom reads and index sequencing primers and use “CTGTCTCTTGATCACA” for adapter trimming which could be full or partial recognition sequence of transposase. Nucleotide BLAST for adapter sequence brings up lots of hits.
From the text of the patent application:

Quote:
Using bioinformatics means, the IRL sequence for the transposase was identified as 5'-ctgtctcttatacacaat-3' (SEQ ID NO:9) and the IRR sequence as 5'-acttgtgatcaagagacag-3' (SEQ ID NO:4). Through experimentation, a modified 19 bp IRR sequence 5'-agatgtgatcaagagacag-3' (SEQ ID NO:5) proved to be more efficient and was used in most experiments.
So the sequence you provide is consistent with Agilent using the Vibrio harveyi IS4-like element.

But, I guess the question still remains -- how non-biased is its insertion? It could be that by adding Mn ions the insertion specificity became lower. It certainly looks that way from the figures in the patent. But it may be just as high as Tn5 in Nextera.

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Phillip
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