Hi Karin, Didn't any of the isolation kits work? 

I do it on single embryoes, I just included an extra wash since I imaged the embroes in benzylbenzoate, then washed with Methanol, before using this procedure. Something went wrong because I have no PCR product, and I guess it must be the extraction since this was the only thing that was different, this usually works with not fixed embryoes. 

DNA extraction from embryo

array single embryos (24hpf to 5-day-old)  in 96-well plate, remove medium

add 25 μl of  100% Methanol, incubate at room temperature for 5 min

Incubate at 80C in PCR machine for 5 min until methanol evaporates, don’t seal the PCR plate and use the lid of PCR machine.

add 9.5ul of TE-Tween-20 ( 10mM Tris, 1mM EDTA pH8.0, 0.33%Tween-20) and 0.5ul of 10mg/ml Proteinase K to each well   (Make a master mix)

Seal the PCR plate with film, incubate at 56C for at least 2 hours or overnight in PCR machine

Incubate at 98C for 10 min to inactive PK

Add 10 ul of H2O, mix well

Sit the plate for at least 10 min before proceeding to PCR

Use 5 ul of DNA for each 20ul of PCR reaction

I have used hot NaOH method of extraction for embryos post insitu hybridization. This has yielded good quality DNA for PCR. I have attached the paper that describes this method. Best wishes