Do we know / have we figured anything out about this room (wood flooring, bookshelf lined, center-ish pedestal)? Someone somewhere here called it an enchantment room, comparing it to something along that line from Minecraft, but I haven't been able to (figure out a way) to use it to enchant anything. Release notes for 0.5.5b refer to "rooms with new “flavors” (studio, graveyard)". Is this room just a flavor room / dungeon decor?
I was thinking maybe you'd need to drop an item on the altar, a scroll of upgrade or maybe weapon upgrade, and maybe a seed or a potion to choose which enchantment you want, then kill an appropriate enemy when they're standing on top of the whole thing... of course, I haven't tried this, and have no reason to believe it would work. But, if you want to try something new next time around, post the results!