Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development. Overall design: ACE-seq was perfomred on (i) 24 hpf, 48 hpf, 72 hpf embryos and adult tissue (tube feet) of purple sea urchin in biological replicates (ii) 36 hpf, larvae (60-70 hpf), juvenile (3-4mo) and adult tissue (liver) of european lancelet in biological replicates (larvae and juvenile stages) (iii) zebrafish 24 hpf embryo.