Samus needs to be in a standing or walking position with no vertical speed on the first frame in the next room, while taking damage through the transition.
This is typically done by using an enemy as a platform beneath the door and instantly standing up by pressing forward while crouched.
Getting Samus into the crouch position can usually be down by spinjumping (beneath the transition tiles) then aiming down to stand on the enemy.
Unmorphing when on top of the enemy will also put Samus in a crouch.
See also: Tech Page