Does anyone routinely do RNA isolation from zebrafish embryos?

I have embryos from different stages but all below 24hpf. This is the protocol I follow:

  1. Take 10-20 embryos
  2. Wash once with milliQ water
  3. Treat with 1mg/ml Proteinase-K (5min with gentle shaking) to dechorionate
  4. Wash again with milliQ water
  5. Remove water and add 250 µl Trizol
  6. Homogenize by pippeting
  7. add 750µl more of trizol
  8. Do the standard trizol extraction step (with chlorofom)
  9. Take the aqueous phase and wash again with 200µl chloroform
  10. Precipitate RNA with isopropanol
  11. Wash thrice with 70% ethanol
  12. dissolve in nuclease free water

Despite all this I get a poor A260/A230 : ~0.4

Moreover, this happens consistently in all samples. The RNA bands look fine on the gel.

I have done RNA isolation many times from cell lines and tissues and never faced this problem. Is this common with zebrafish embryos? Is there a way to fix this other than by using kits?


2 Answers 2


Usually I had no problems with RNA extractions - from various cultured cells as well as a number of different tissues from mouse. If I look at your protocol this is pretty much the same as the one we used or the one recommended here for zebrafish embryo. This protocol "Purification of RNA Using TRIzol (TRI Reagent)" seems also interesting.

What can happen is a contamination by phenol or carbohydrates, then we usually used the protocol below to clean up the sample. You can also use column based methods, but they are more expensive.

  • add 1/10 vol of NH4OAc (5M), 2.5 volume 100% cold EtOH (100%) and 10µg glycogen (for total RNA we usually didn't use any co-precipitation agents) and mix well
  • incubate 30 min at -80°C
  • centrifuge 20 min at 12000g at 4°C and remove the supernatant
  • wash with 75% ice cold EtOH
  • centrifuge 5 min at 12000 g at 4°C and remove supernatant
  • Re-suspend the pellet in RNAse free water (can take some time)
  • $\begingroup$ well. I had also tried precipitating with 0.1 vol 5M LiCl + 2.5 vol EtOH.. Still same problem.. If it is a phenolic contamination it should go away in the second chloroform wash. This is persistent. $\endgroup$
    Jan 10, 2014 at 5:06
  • $\begingroup$ Are your embryos pigmented? $\endgroup$
    – Chris
    Jan 10, 2014 at 7:27
  • $\begingroup$ No.. they are very early embryos.. not pigmented at all.. $\endgroup$
    Jan 10, 2014 at 9:19
  • $\begingroup$ Ok, this excludes melanin contaminations. This is pretty strange. $\endgroup$
    – Chris
    Jan 10, 2014 at 13:11
  • 2
    $\begingroup$ Thats better. This paper says that the quality is going down when the homogenzation is incomplete and recommends the homogenization of frozen embryos. $\endgroup$
    – Chris
    Jan 17, 2014 at 10:25

This addition to the protocol worked out and good RNA quality was obtained:


  • Homogenized the embryos, suspended (and frozen) in trizol by passing through 2ml insulin syringes. (About 10 times).


  • Washed 2 times with 500µl 80% Ethanol
  • Washed 3 times with 500µl 70% Ethanol

Dechorionation was dispensable and Proteinase-K treatment was too harsh on early stage embryos. So I did not dechorionate this time.

I think the number of washes can be reduced (1×80% and 2×70%) but this is what I stuck to (out of superstition :P)

  • $\begingroup$ Ah, good to know the solution to this. My guess would also be that the number of washes can be reduced. I wash like this for my tissue samples. $\endgroup$
    – Chris
    Oct 19, 2014 at 15:33
  • $\begingroup$ AS you mentioned before, the problem was I guess homogenization. But insulin syringe is a good tool when you have lots of samples and works better than the hand held homogenizer (in this case) . $\endgroup$
    Oct 20, 2014 at 5:21
  • $\begingroup$ I'll keep this in mind. $\endgroup$
    – Chris
    Oct 20, 2014 at 6:59

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