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  • Arvind Bhagwat
    Junior Member
    • Nov 2010
    • 8

    #1

    Optimal fragmentation of bacterial mRNA

    Would any one please share conditions used for fragmenting bacterial mRNA? I am shooting for ~200 nt and starting mRNA conc. is ~75-100 ng/. I am using NEB Next mRNA library kit. They recommend 5 min at 94 C in Mg buffer. However this is for eukaryotic mRNA. I will appreciate if someone could share their success story using this kit with bacterial (E. coli/Salmonella/Bacillus ...) mRNA. I have depleted total RNA using Epicenters Ribo-Zero kit. Thanks everyone!
  • ZWB
    Member
    • Apr 2011
    • 27

    #2
    I've been successful using the NEBNext fragmentation kit with an incubation of 3 minutes instead of 5. Make sure to use only 200ng/rnx (or less) and pool multiple rxns during cleanup. This has worked well for total or rRNA depleted samples from a variety of Gram negative bacteria.

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