I'll try for an answer with the approaches I feel might work for you. Generally it might be helpful to not let the dog go into the sleeping room at all (day and night)l if that's an option for you.
Approach 1 (Barrier):
Leave the bedroom door open at night but do not let your dog enter the bedroom. If your dog is persistent on going in you can practice this during the day so you don't lose too much sleep over it. Other than that blocking the door with an obstacle the dog can't pass should help you keep her out. Leaving the door open can be a permanent solution, if you feel comfortable with it. Otherwise try to close the door a little more every few days until it is completely closed. The idea here is that you don't cut all stings loose immediately and the dog can observe you (while being in another room) and realize that she doesn't miss out on anything when she isn't with you during the night.
Approach 2 (comfort):
You can leave a piece of clothing, a toy, etc. with the dog, either in her bed or next to her bed. The point here is that your scent is very present even when you are not, which helps your dog feel comfortable and protected. In addition I would place the bed somewhere where the dog is able to observe most of your home, especially your bedroom door. This way she can't "miss" you leaving the bedroom.
Approach 3 (routine):
Try to have as much of a bedtime routine as possible. This will reassure your dog that yes, you will leave but you will also be back in the morning. Leaving for bed shouldn't be an unexpected twist of events for your dog.
My personal routine with my dog is to go on a short walk, get myself ready for bed, tell my dog to lay down in her bed (if she doesn't already), pet her a bit and say "goodnight", then I leave for bed. It works well for us. You'd obviously have to find your own routine that works for everyone in your household.
Other than this, observe the routine that you have or don't have at the moment. Is your dog fine until you close the door or is she nervous beforehand? You should adjust your routine to make sure the dog is fine with you leaving in the first place (meaning your dog is relaxed before you close the door). Maybe make giving your dog something to chew on part of the routine if you feel it will help your dog cope.
Approach 4 ("casual" separation anxiety):
Of course you can also treat this like "casual" separation anxiety and try to work through it like that. This issue is widely discussed, so I won't lay the whole training out here as it isn't an exact answer to the specific question seeing as your dog is generally fine being left alone.
View this example to train being alone with your dog.
Obviously these approaches can be combined and there is not a general solution to this. You just have to find out what works best for you and your dog. This is nothing but a collection of ideas to help you find a way to cope with the problem. The most important thing is that you are comfortable with the approach you are taking.
Oh and as always, rewarding desired behaviour is good no matter how you work on this with your dog and giving in to the dog whining (or whatever other bad behavior she might come up with) is never a good thing.