In the past I have used NEB's Ultra II DNA Library Prep kit for whole genome library construction. I used the Covaris ultrasonicator for shearing. I wanted to try switching to enzymatic shearing instead, so I have been trying NEB's Ultraexpress FS DNA library prep kit. However, I am finding it difficult to get the insert sizes I want. First I tried adjusting the bead concentrations to 0.5x and 0.6X, but ended up with very low concentration libraries. Then I tried the 0.6x and 0.7x bead concentrations and got better yield but the library peak was around 360, which is lower than I would like (peak insert size would then be 240, which would lead to overlap when doing 2x150 sequencing.) Does anyone have advice on how to get larger insert sizes while not losing too much of the library yield? I am considering just going back to the Covaris tubes, so at least I could still use all the NEB indices I bought. But for the future, do you have different enzymatic kits your prefer? That give larger insert sizes? It looks like Illumina's Nextra kit gives larger insert sizes for example. I would appreciate any thoughts you have! Thanks! Karen
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