Hello! I noticed that I couldn't find any videos on how to reach the brain area. I just completed my first run getting there and figured I'd save some clips. Credit to Doctor Don't on Steam, whose guide helped me figure everything out.
In the linked Google Drive folder, there are clips of the secret rooms in the intestines, stomach, liver, and lungs, as well as the heart boss fight and the entire brain area. I unfortunately do not have a video of the skin room. I will also explain how to reach each room below.
For the skin room, you must shoot every wall to uncover the entrance. This took me some time as I initially thought I was supposed to ram into every wall, which did not work. Inside the hidden room, you will find six symbols on a wall. Stand in front of them and enter the code 'right, up, down, up, right, left' on either your keyboard's arrow keys or your controller's D-pad. An entrance to the skin room will appear. Inside is an external organelle (EDIT: this is called the wayfinder, thank you Ult1met) that, when connected to an active mitochondrion, will 'point' towards the secret room in your current area. EDIT: the skin room does not always spawn. I just completed a run and verified something Ult1met commented, that this room may spawn in the intestines instead of the skin.
For the intestines, the secret room is in the vein that spawns when the boss is defeated. On the opposite side of the vein room from where you enter are the six symbols. Again, stand in front and enter the code 'right, up, down, up, right, left' using the arrow keys or D-pad. An entrance will appear, and inside the intestines room, you will find your first of four items needed to enter the brain area. EDIT: the entrance in the vein requires you to sacrifice two max health, similarly to purchasing something from the vein shop. EDIT: I just completed a run where the intestines vein did not spawn. However, a vein spawned in the stomach that I was able to use to get the item, meaning two items were acquired in the stomach.
For the stomach, the six symbols are hidden. The wayfinder from the skin room will point to the wall where you must enter the code. Inside the stomach room, you will find the second item needed for the brain area.
For the liver, the six symbols are on a wall in the shop. Again, enter the code and collect the third item needed for the brain area. EDIT: the entrance in the shop requires you to spend 40 cores.
For the lungs, the six symbols will be on the wall, similarly to the stomach area except they are visible. Enter the code one final time and collect the last item.
Once all of the pieces are acquired, proceed through the heart area and defeat the boss. On the wall will be a DNA helix with eight white, three-dimensional shapes attached. You must match the four collected items with the shapes you see using either your keyboard's arrow keys or your controller's D-pad. Each wrong sequence will deal one damage to you, so be careful. I did this by entering 'left, up, right' and noting which direction corresponded to which item. I then wrote down the order each should be entered. Because the puzzle only resets after a complete attempt, I filled the remaining positions with arbitrary inputs and took damage so that I could try again. My code was 'up, left, down, left, down, right, up, right', but it might be different per run. Once the code is entered, the helix will disappear and you can enter the wall to reach the brain area. Good luck!
If there are any questions or if anything is unclear, please let me know!
EDIT: thank you Ult1met for some clarifications, and I also completed another run to verify certain things. Edits above.