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(Source: D. Ellies from Zebrafish Book 5th Edition)

This rapid, simple procedure yields DNA and RNA, which can both be seen on a normal Agarose gel. Remove the unwanted nucleic acid with the appropriate nuclease.

Buffer (use RNAse free reagents!)

• 100 mM Tris-HCl (pH 8.0)
• 100 mM EDTA
• 250 mM NaCl
• 1% SDS

NOTE: You do not need to remove embryos from their chorions.

For a single embryo:

1. Rinse embryos in sterile water.
2. Homogenize in 10 μl of buffer by hand with a sterile pipette tip.
3. Add 90 μl of buffer and homogenize again.
4. Extract with 50 μl of phenol:chloroform:isoamyl-alcohol (50:48:2). Mix gently by inversion, centrifuge and collect top aqueous phase.
5. Extract aqueous phase as above but with 50 μl of chloroform:isoamyl-alcohol (24:1).
6. Add 25 μl of NaAcetate 3M pH 7 and precipitate with 200 μl of ethanol.
7. Resuspend pellet in 20 μl of TE.

For 5 or more embryos:

1. Rinse embryos in sterile water.
2. Homogenize in 100 μl of buffer by hand with a sterile plastic pestle
3. Add 300 μl of buffer and homogenize again.
4. Extract with 200 μl of phenol:chloroform:isoamyl-alcohol (50:48:2). Mix gently by inversion, centrifuge, and collect top aqueous phase.
5. Extract aqueous phase as above but with 200μl of chloroform:isoamyl-alcohol (24:1).
6. Add 100 μl of NaAcetate 3M pH 7 and precipitate with 800 μl of ethanol.

NOTE: with 5 or more embryos, the nucleic acid precipitate is immediately visible and can be centrifuged right away.

7. Centrifuge and resuspend pellet in 20 μl of TE.