Mouse Perfusion



New to this site so apologies if this topic has been discussed already

I usually work with rats but have started to incorporate mice into my research recently. Will have to peruse mice soon but have not done it before. I’m well trained in rat perfusion but wanted to ask a few things about mice:

  1. The needle I have to pierce rat heart looks to be too big for mouse. What do people generally use? Is it clamped in place?

  2. Is the needle inserted all the way into the ascending aorta? I do this in rats as it’s quire easy to see, but I imagine it might be more difficult in mice.

  3. What volume of saline and PFA do people use in mice? For rats I generally use 150 ml of each.


  1. I’ve traditionally used things in the 25 gauge 3/4" range. In this group here, some folks clamp and some folks hold. I tend to hold as I’ve got control issues…and the motion to place a clamp is more trouble that is worth for a quick perfusion.
  2. If you can get it into the ascending aorta without piercing it, that’s great. It helps to dull the bevel of the needle sometimes to help. It’s more a matter of skill than desire though, as we would all love for it to be right in the ascending aorta to reduce retrograde flow into the pulmonary vasculature.
  3. 10 mL is enough. I like 20 mL though. Mice generally only have about 1 - 2 mL of blood in them, so either is a large amount.

Hope that helps,


Great thanks for advice, it’s a big help.



@DaraBree: Welcome to the forum. @YawarJQ said pretty much everything I was going. Thanks Yawar!
I generally perfuse 50 ml of 4% PFA. Most people perfuse PBS first to clear the blood. That requires either changing syringes or having a three-way stopcock to push PBS first, then PFA. I actually just directly perfuse with PFA. Maybe there is some blood left, but it doesn’t seem to affect much. A lot of blood gets flushed out and the mouse still gets perfused with PFA well. But if you can coordinate the PBS + PFA, it probably doesn’t hurt.

I’ll post a video later.


Hi @achamess,

Thanks for the tips and the video. It’s a great help.