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This protocol explains how to extract DNA from a single zebrafish embryo.

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[Bio101] Zebrafish Embryo DNA Preparation

Molecular Biology > DNA > DNA extraction
Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
2/20/2012, 9310 views, 0 Q&A
DOI: http://dx.doi.org/10.21769/BioProtoc.184

[Abstract] This protocol explains how to extract DNA from a single zebrafish embryo.

Materials and Reagents

  1. Proteinase K (Roche Diagnostics, catalog number: 03115836001)
  2. 1 M Tris (pH 8.3)
  3. NaCl
  4. KCl
  5. CaCl2•2H2O
  6. MgSO4•7H2O
  7. Sterile water
  8. 10%Tween 20 (EMD Biosciences, catalog number: 655207)
  9. 10% NP40 (Merck KGaA, catalog number: 492018)
  10. Embryo lysis buffer (see Recipes)
  11. 1x PCR buffer (see Recipes)
  12. E3 (see Recipes)


  1. PCR Thermal cycler
  2. Centrifuges
  3. Incubator
  4. 96-well plate


  1. Freezing single live embryos
    1. Wash dechorionated embryos 3x with E3.
    2. Place a single embryo into a well of a 96-well plate and remove all excess buffer.
      (Store dry at -20 °C if needed).

  2. DNA preparation:
  1. Add 50 μl lysis buffer to single (live or in situ'd) embryos.
  2. Incubate at 98 °C for 10 min to lyse cells. Spin down.
  3. Add 5 μl Proteinase K (10 mg/ml stock) to single embryos.
  4. Incubate at 55 °C for at least 2 h (longer the incubation, cleaner the DNA).
  5. Incubate at 98 °C to heat kill Proteinase K.
  6. Vortex thoroughly and spin down debris.
  7. Use 2 μl of single embryo DNA per PCR reaction.


  1. 1x PCR buffer
    For 50 ml
    10 mM Tris-HCl (500 μl of 1 M Tris) (pH 8.3)
    50 mM KCl (2.5 ml of 1 M KCl)
    47 ml sterile water
    (Can be stored at RT for severalmonths)
  2. Embryo lysis buffer (1x PCR buffer with tween 20 and NP40)
    For 10 ml of lysis buffer
    9.4 ml 1x PCR buffer
    300 μl NP40 (10% stock) ***Make fresh
    300 μl tween 20 (10% stock) each time***
  3. E3
    60x E3 stock (2 L)
    NaCl                 34.4 g  
    KCl                   1.52 g
    CaCl2.2H2O      5.8 g
    MgSO4.7H2O    9.8 g
    Add distilled water up to 2,000 ml.
    Store at RT.
    To dilute to 1x for rearing zebrafish, use 160 ml of stock and fill to 10 L with ddH2O


This protocol was developed in the Michael Granato Lab at University of Pennsylvania, Philadelphia, USA, and this work was supported by NIH grant R01HD037975.

How to cite this protocol: Jing, L. (2012). Zebrafish Embryo DNA Preparation. Bio-protocol Bio101: e184. DOI: 10.21769/BioProtoc.184; Full Text

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