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    CTAB Extraction Protocol for Sediment

    Cameron R. Turner

    Published: 2023-04-07 DOI: 10.17504/protocols.io.ewov1ozkolr2/v1
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    Abstract

    Successfully used by Turner et al., 2015 to detect bigheaded Asian carp surface sedimentary DNA from experimental ponds and natural rivers

    http://www.sciencedirect.com/science/article/pii/S000632071400442X

    Steps

    Sample preparation

    1.

    THAW the CTAB-preserved sediment sample in the fridge for no more than 24h 0m 0s

    DECONTAMINATE the exterior of the sample tube with 10% bleach solution and rinse with reverse osmosis water

    2.

    VORTEX at max speed for 0h 0m 30s

    INCUBATE at 60°C for 0h 10m 0s

    Chloroform extraction

    3.

    ADD 15mL of Sevag (Chloroform/Isoamyl alcohol 24:1)

    Note
    Steps involving Sevag should be performed inside a fume hood.

    4.

    VORTEX the sediment/CTAB/Sevag mixture briefly

    SHAKE at low speed (Vortexer setting 4) for 0h 5m 0s

    5.

    CENTRIFUGE at 3220x g for 0h 15m 0s at Room temperature

    CAREFULLY transfer the supernatant to a new 50 mL tube

    Ethanol precipitation

    6.

    ADD an equal volume of ice-cold Isopropanol to the supernatant

    ADD 1⁄2 volume of 5M NaCl to the supernatant

    INCUBATE at -20°C for 1h 0m 0s (or overnight if more convenient)

    7.

    CENTRIFUGE at 3220x g for 0h 15m 0s at Room temperature

    CAREFULLY pour off the supernatant

    8.

    ADD 2mL of 70% EtOH, washing down the inner walls of the tube

    CENTRIFUGE at 3220x g for 0h 2m 0s at Room temperature

    POUR off EtOH and allow the DNA pellet to air dry completely (a 45°C incubator can be used to evaporate stubborn droplets)

    DNA resuspension

    9.

    RESUSPEND the pellet in 1000µL of LoTE buffer. Heat briefly at 45°C and swirl gently to mix and resuspend. Once fully resuspended, briefly centrifuge to collect all liquid in the bottom of 50-mL tube.

    10.

    Transfer all liquid to a 1.5-μL low-bind microcentrifuge tube

    11.

    Use 200µL in OneStepTM Inhibitor Removal Kit (Zymo Research, Irvine, CA)

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