Apoptosis via TUNEL (Veenstra lab)
See: Veenstra et al. (1998) Cell Death Diff. 5:774-784 protocol adapted from Blaschke et al., (1996) Development 122, 1165-1174. Submitted by Gert Veenstra.
Fixation and pretreatment
Dejelly albino embryos carefully in 2% Cysteine (pH 7.8).
Remove the vitellin membrane with two pairs of tweezers (or carefully pierce multiple times after fixation)
Fix the embryos in MEMPFA for 1 hour at room temperature
(MEMPFA: 100 mM MOPS pH 7.4, 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde)
Wash 2 times 30 minutes in methanol, store in methanol at -20 °C.
Wash embryos 2 times 15 minutes at room temperature in PBT
(0.2% Tween in phosphate buffered saline (PBS))
Wash embryos 2 times 15 minutes at room temperature in PBS
Wash embryos 30 min. in TdT buffer (Gibco) 1 hr. at room temp.
Incubate embryos overnight at room temp., in TdT buffer containing 0.5 µM digoxygenin-dUTP (Boehringer) and 150 U/ml TdT (Gibco).
Wash 2 x 1 hr. with PBS/EDTA (1 mM), at 65°C
Wash 4 x 1 hr. with PBS at room temp.
Detection and chromogenic reaction
As for in situ hybridization, see:
Harland,R.M. 1991. In situ hybridization: An improved whole mount method for Xenopus embryos, vol. 36. Academic Press Inc., San Diego, pp. 685-695. 
Or for a fluorescent protocol see Vize et al., 2009.