Zebrafish Embryos can be cryopreserved: see attached paper. If in doubt, cryopreserve your embryos and then do the RNA extraction when needed. 

We routinely store samples for later analysis in TRIzol.  As long as you are working in RNAse free conditions you should be fine.  You may consider homogenizing the tissue in the TRIzol prior to freezing, but it is not completely necessary if you are using the appropriate volume for your number of cells/size of tissue. Once it is in the TRIzol it is completely stable at -20C for several weeks.

We have had issues with RNA purity after TRIzol purification (usually contaminating TRI-reagent), but cleaning up over an RNA column always solves this.  Typically putting the samples in TRIzol is the most expensive step, so we only do it if we are reasonably sure that we will analyze them at a later date.

Hi all,

Thank you very much for you input. After your suggestions and others this is what I end up doing, and i worked very well:

I extracted from pools of 10, 20 and 40 3dpf embryos and got around 250 ng RNA/fish and a RIN of 10 for all samples. 

BR

Sanna

Is your RNA-seq work well?