poor RNA quality from zebrafish embryos
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)