Wholemount in situ hybridisation

Based on Wilkinson protocol, modified by Murray Hargrave (m.hargrave@cmcb.uq.edu.au), Koopman lab


1 Mix in the following order at room temperature:

2 Incubate at 37C for 1 hour, then add another 20U of RNA polymerase.

3 Incubate for a further hour at 37C.

4 Remove a 1L aliquot and run on a 1% agarose/TAE gel to estimate the amount synthesised. An RNA band of approximately 10 fold greater intensity than the plasmid band indicates that ~10g of probe has been synthesised.

5 There are two successful methods for purification of the RNA probe:

A) for the lazy (this works fine):


B) for the paranoid:

6 Redissolve pellet in DEPC milliQ H2O at ~0.1g/L and store at -20C.




Day 0

1 Dissect embryos in ice-cold PBS. Try to remove as much of the extraembryonic membranes as possible. Be sure to remove or at least puncture the amnion and in embryos of 10dpc or older, puncture the head with a syringe needle to avoid trapping of reagents in the lumen.

2 Fix in 4% paraformaldehyde (PFA) in PBS at 4C overnight.

Varying the fixation time from 3h to overnight has no effect on signal or background.

3 Wash twice with PBTX for 10 minutes each at 4C.

4 Wash with 50%, MeOH/PBTX, then twice with 100% MeOH for 10 minutes each.

Can store the embyros at 4C or -20C at this point, for up to a few months, or preferably in pre-hyb (see step 12).


Day 1

5 Rehydrate by taking the embryos back through a MeOH/PBTX (75%MeOH -> 50% MeOH -> 25% MeOH -> PBTX) series in reverse

6 Wash twice with PBTX for 10 minutes each.

7 Treat with 10g/mL ProteinaseK in PBTX for 5-20 minutes at room temperature.

The length of this treatment depends on the size of the sample and the batch of proteinase K. Each batch should ideally be tested. As a rough guide, use 5 min for E7.5, 7 min for E8.5, 9 min for E9.5, 11 min for E10.5, 12-14 min for E11.5.

8 Wash twice with PBTX for 5 minutes each.

Be careful - the embryos are fragile!

9 Refix with fresh 0.2% glutaraldehyde/4% PFA in PBTX for 20 minutes.

10 Wash twice with PBTX for 10 minutes each.

11 Place in a 2ml screw cap eppendorf tube and fill with prehybridisation mix, and allow the embryos to sink, replace prehyb soln.

12 Incubate at 65C for 2h.

This step can also be performed overnight. Alternatively the embryos can be stored in this solution at -20C.

13 Remove prehyb and add hybridisation mix including 1.0 g/mL DIG labelled RNA probe.

If high background is seen, probe concentration can be decreased to 0.5 g/mL.

The tube needs to be full so that probe does not dry onto the sample.

14 Incubate at 65C overnight.

If the probe is short or heterologous, 55C can be used for pre-hyb, hyb and stringency washes.


Day 2


From this point on RNase-free conditions are no longer necessary.

1 Wash with the following for 5 minutes each at 65C (or 55C)

During these washes, start preabsorbing the antibody as described below.

2 Wash with 2xSSC, 0.1% CHAPS twice for 30 minutes each at 65C (or 55C).

3 Wash with 0.2xSSC, 0.1% CHAPS twice for 30 minutes each at 65C (or 55C).

4 Wash with TBTX, twice for 10 minutes each at room temperature.

5 Preblock the embryos with 10% sheep serum, 2% BSA in TBTX for 2-3 hours at room temperature.

6 Remove the 10% sheep serum, 2% BSA from the embryos and replace with the preabsorbed antibody (see below). Rock overnight at 4C.




1 During the washing of the embryos (step 1 above), weigh out 3mg of embryo powder into a microtube, add 0.5mL of 10% sheep serum, 2% BSA in TBTX and 1L anti-DIG-AP Fab fragment (Boehringer 1093274).

Embryo powder should match the species being studied.

2 Rock gently at 4C for 3 hours or longer.

3 Spin in a microfuge for 10 minutes at 4C.

4 Dilute the supernatant to 2mL using 10% sheep serum, 2% BSA in TBTX.

5 Store at 4C until use.



Day 3

1 Wash at least five times with TBTX containing 0.1% BSA for 1 hour each at room temp.

The antibody solution can be kept at 4C and reused up to 4 times.

2 Wash overnight at 4C with TBTX containing 0.1% BSA.

This wash is optional but usually convenient.


Day 4

3 Wash twice with TBTX for 15 minutes each.

4 Wash three times with NTMT for 10 minutes each.

5 Incubate with NTMT including 4.5L NBT and 3.5L BCIP (X-phosphate) per mL. Rock for the first 20 minutes then transfer the embryos to a glass embryo dish or scintillation vial.

Avoid using a plastic petri dish as crystals tend to form.

Keep in the dark as much as possible and allow the colour reaction to proceed until signal is strongest without producing background staining.

It is best to slightly overstain, as subsequent washings will tend to destain samples. If samples are to be sectioned, overstaining is recommended. You can stop the colour reaction by washing in NTMT, then TBTX overnight, then re-start the colour reaction the next morning.

6 When the colour has developed to the desired extent, wash with NTMT then with PBTX.

7 Wash several times in PBS with 1% Triton X-100.

This will blue the stain and decrease background and signal. Some observation and judgement is required here. For weak signal, this step can be shortened or omitted. If signal is strong and background is weak, then a total of a few hours is recommended. Overstained or high background samples can be washed for up to several days.

8 Fix the stain by incubating the embryos in 4% PFA in PBTX overnight at 4C.

9 Photograph embryos as soon as possible.

The signal can fade or the enitre embryo can turn blue upon storage. Position embryos, immersed in PBS, in grooves cut in a layer of agarose in a petri dish. Adjust lighting to optimize the translucency of the sample.

10 If the embryos are to be stored for extended periods, use PBS containing sodium azide, or take them through a PBTX/glycerol series into 100% glycerol.



This must be made fresh on the day of use as pH decreases during storage due to the absorption of CO2.

It is best to let these reagents warm to room temperature before use as it may decrease the amount of crystal formation in the colour reaction.



Wilkinson, D.G. (1992) Whole mount in situ hybridization of vertebrate embryos, in In situ hybridization: A Practical Approach (D.G. Wilkinson, ed) pp 75-83, IRL Press, Oxford.