It seems in electrophoresis, agrose gel always runs horizontally, and SDS-PAGE gel always runs vertically, why?
When you stand general agarose gel vertically, the gel is slippery coming out from the bottom; although, some run vertically.
To polymerize acrylamide, it is good idea to avoid air because oxygen inhibits polymerization of acrylamide. You would get an air tight condition, pouring acrylamide between glass plates, but how could you run gel made between glass plates. When you set such gel plates horizontally, how do you load samples? Then, it is easier to set gel plates vertically.
Generally, one would want to run all the gels vertically to save the space. The gel slab has to either support itself or be enclosed in a supporting structure, like between glass plates. Simple agarose electrophoresis wouldn't benefit from enclosure into a precisely defined glass enclosure, and agarose is not strong enough to be run vertically - the slab will not support itself. Thus PAGE gels are run vertically and agarose - horizontally.