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    Genomic DNA isolation from fixed cells

    Suzanne R Pfeffer, Herschel Dhekne, Ebsy Jaimon

    Published: 2022-09-24 DOI: 10.17504/protocols.io.eq2lynm9qvx9/v1
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    Abstract

    This protocol details the procedure of genomic DNA isolation from fixed cells.

    Attachments

    iugzbc32f.docx

    Steps

    Genomic DNA isolation from fixed cells

    1.

    Resuspend 1-3 X106 cells in 250µL of PBS and transfer to a 2 mL tube (this would represent one 3.5 cm dish of 3T3 cells).

    2.

    Add 200µg Proteinase K (from a 20mg/mL stock) and 200µg RNase A (from a 20mg/mL stock).

    3.

    Incubate cells at 37°C for 0h 30m 0s in a water bath.

    4.

    Add 250µL Qiagen AL lysis buffer per 250µL of the protease and RNAase-containing cell suspension and mix thoroughly.

    5.

    Place tubes in an incubator at 56°C with shaking at 800rpm,0h 0m 0s , capped.

    Note
    Each tube is parafilm sealed to ensure safety.

    6.

    Add 250µL, 100% molecular biology grade ethanol; mix slowly using a slow vortex for 0h 0m 5s.

    7.

    With a razor blade, trim the tip of a 1mL pipet tip to enlarge the opening. Use this tip to pipet out DNA from the ethanol solution and apply it onto a silica spin DNA binding column (e.g. EconoSpin 1920-250).

    8.

    Spin at 6000x g,0h 0m 0s for 0h 1m 0s in a fixed angle tabletop microfuge; aspirate and discard flow-through.

    9.

    Add 500µL Qiagen buffer AW1 to the column, spin again at 6000x g,0h 0m 0s for 0h 1m 0s, aspirate and discard flow-through.

    10.

    Add 500µL Qiagen buffer AW2 , spin at 8000x g,0h 0m 0s for 0h 1m 0s, aspirate and discard flow-through.

    11.

    Spin once more using microfuge to remove excess ethanol at 13000x g,0h 0m 0s for 0h 1m 0s.

    12.

    Transfer column into a new, 1.5 mL collection tube.

    13.

    Elute with pre-warmed, 100µL nuclease-free water or TE .

    Note
    Volume depends on starting number of cells: use 100µL per 1 million cells.

    14.

    Incubate for 0h 1m 0s, then spin at 13000x g,0h 0m 0s for 0h 1m 0s.

    15.

    Add another 50µL nuclease free water to accomplish a second elution.

    16.

    Incubate at Room temperature for 0h 1m 0s, then spin as before at 13000x g,0h 0m 0s for 0h 1m 0s.

    17.

    The two flow-through fractions contain the genomic DNA .

    18.

    Perform Nanodrop and Qubit HS DNA estimation to calculate yield.

    Note
    Theoretically, 1X106cells should yield 6µg DNA.

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