Welcome to the Reactor Room!
Don't go down the hallways.
Don't drop your reactor cores.
Don't get caught sleeping when the mutants come for YOU.

I hadn't seen a guide for this aspect of the game, so here's what I did!

My game details:
Day 41, Global infection 44%, Normal Mode, Tech level 2+.
I lost count of the number of invasions I've had, but they seem to happen every couple of days after hitting 30% global infection. If you can keep your global infection lower than that, you don't need this guide!

This is your Reactor status screen.
Here I am prior to Invasion:

Here I am after I got done with the fight:

Not too bad! Only lost 268 power to damage, and nothing was broken.

If you look close, you can see that Turrets 7 and 8 are higher level. I spend most of my time defending the room down between them. It's important to have as much fire power down there as possible, because everything will be trying to get down there, and those turrets won't have to sweep their ranges to hit it.

On to the Basics. We'll get to barricading in a little bit, I promise.

The invasion timer seems to range between 10 and 4 hours. The Timer doesn't seem related to Global infection percentage as of 2/16/2016, but my game started before that so your mileage may vary. The STRENGTH of the invasion DOES scale up. The more you've had, and the higher the global infection, the worse they will be.
Likewise, all screeshots were taken based on the game started prior to 2/1/2016.

1) DON'T PANIC! You have time to get back to base. If you already set your barricades, finish a floor or two. If this is your first invasion, a bit or prep won't hurt, but you could do it afterward too.

2) REPAIR YOUR WEAPONS! Do this first when you come back. It takes time, and you can do other things while it happens. Like NAP. Or dump resources at Engineering from the run you just did and then NAP.

3) TAKE A NAP. You are probably tired from exploring. Guarding the Reactor room requires stamina and running around. Make sure your fatigue will be less than 60% for the fight. West can recover ~30% stamina per hour, so plan accordingly!

4) BUILD SMGs ONLY IF YOU NEED THEM. I scrounged up most of my cores, and I haven't even explored several sectors yet. I had to make barrels and heatsinks. I've put in my old personal SMGs as I've upgraded. DON'T make Barrels or Heatsinks that require more than 50 Link for your turrets. SMGs do great with heat, so even the most basic heatsink is fine. Better barrels give more crits, but that may not be worth the cost.

5) TURN ON THE TURRETS! They are useless unless you hit the power switch just off the South entrance to the Reactor room. LISTEN to them too. You can see half at a time, so if you hear them but can't see them, you need to move, NOW.

6) PHARMACOLOGY IS YOUR FRIEND. A single Marsmari and Windroid may get you through the entire fight, and will hopefully keep Big Fat from sneaking up and breaking your legs. Watch out!

PRIORITIZE WHAT YOU SHOOT! Turrets are stupid, and miss moving targets most of the time.

1. Take out SMALL stuff for them. This means Bug Moms to get rid of the little ones that bite you and the Reactor, and (much later) Eyeballs. USE YOUR PISTOL, or SMG if closer.
   
2. Take out Spitters, or at least get their attention. They will stand at a corner and just ping at a reactor core otherwise. The big ones will be out of turret range unless they chase you some.
   
3. Whatever happens to be charging you. DODGE! Pull out that shotgun & shoot. DODGE AGAIN if it isn't dead. Use an SMG if you need to. I hope you took that Marsmari and a Big Fat isn't about to break a leg from behind.

MOVE AROUND. If you can HEAR a turret, but can't see it's target, then MOVE. This means you will be constantly moving around to acquire and kill or just bait something to come get you.
If it is chasing you, it isn't beating on your Reactor!

BE CAREFUL ABOUT REACTOR CORES. You will probably lose a few. If you really, REALLY don't want them damaged, then strap them to your body for safekeeping...it just makes you a more radioactive attractive target. Do too many and you might get swarmed.

Below is the basic arrangement which has worked for several invasions now.
If a room in Central station had a double door, you can bet I dragged 80% of the stuff out. I didn't bother with chairs. I DID drag the couches out of the bedrooms.
All that dragging took about 10-20 hours in game time!

Important thing to remember:
Barricades are mostly to SLOW things down. They won't stop the mutants from getting to your Reactor Cores if you just leave the area completely alone.

1. That's why you have to MOVE, to attract things to you.
   
2. That's why you shoot Bug Moms, so the little Biter Bugs can't find a small gap and make it a larger one! As of 2/16/2016, 3 little Biter Bugs can push JUST as hard as a Big Fat, and they are much smaller so they can find little gaps nothing else can get into.
   
3. Turrets help even when you can't, and slowing things down/sticking it to a spot is exactly what a turret needs to hit them.

That said, I've had quite a bit of success with my current layout.

We will start in the North East corner and go counter-clockwise from there!
But wait, there's nothing here! That's right, I couldn't effectively barricade an entire 1/4 of the room! Mutants just LOVED both cores here. They come from the North and East, seeming to prefer this corner for attack in my game.
The Reactor Core there is bait, and will get pounded unless I clear mutants off of it at least once.

The North West corner
I struggled with this corner for a little bit, but theres very little bodycount here on the north end.
On the north side, vending machines are INCREDIBLY heavy, and not that wide. The vending machine jams on the backside and bottom corner against the reactor core. The Desk overlaps the vending machine and jams against the wall. A Big Fat can't really get into any of those cracks, but three little Biter Bugs could move that vending machine up and away enough to get at the core.

On the West Side, I had a LOT of trouble keeping things off. The L desk wedge against the reactor okay, but aren't heavy. The bigger tables wedge against the wall, but aren't heavy either. Two tablers were not sufficient, and I did lose a core here.

The South West corner
I put my second of three vending machines here, but didn't have the same things to wedge against it. I saw a big fat taking swings at the reactor from behind the vending machine to no effect. If I leave this corner alone, eventually bugs or small stuff works down around the couches to come up from underneath.
The south core here has literally NOTHING around it. With a barricade on one side, and me on the other, not much goes after it.

The South East corner
Another L desk, and another vending machine! This one doesn't work so well, but it's enough.
Again, nothing at the south core, for the same reason as at the South West corner.

Central
Two long couches and an L desk is ALL that is here. I spend most of my time running around the southern half to bait things into chasing me. Big Fats just sort of slide along the couches instead of hitting the cores, although sometimes they get a swing in (notice all the blood around the west most core). I have to move the bottom long couch back into place every time.

If you have an questions, or observations or comments, let me know!