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Old 07-05-2013, 08:31 AM   #2
Calluna
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Location: Seattle, WA

Join Date: Feb 2012
Posts: 12
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I may have done my math incorrectly, but I came up with a final NaOH concentration of 0.002N in your final mixture. If so, that would probably explain the low cluster density/low passing filter. Illumina documents typically say to stay below 0.001M (1 mM) in the final solution after diluting with HT1.

I would recommend reprepping your denature/dilution. Since your libraries are fairly low concentration, you will probably want to denature, but neutralize your final denature with HCl. See this post for more help:
http://seqanswers.com/forums/showthr...+hybridization

Happy sequencing

Last edited by Calluna; 07-05-2013 at 08:36 AM.
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