My memory is that the Omaha-Mankato-Twin Cities line was the Omaha Road (C St.P M & O) and the line across southern Minnesota into South Dakota (later known as "The Alco Line") was C&NW. I don't think there was a train specifically going from Omaha to Rochester, I think you could probably get on a sleeper in Omaha that would be switched onto a Rochester-bound train in Mankato.
Rochester of course was a major destination from all parts of the country, due to the Mayo Clinic.
Not the easiest format to use - but not impossible. Look for the cities you want on the pages at the bottom - that will give you the railroads and timetable numbers (if any). Then find the railroad section. The railroad table of contents is at the top. Then wander through the pages and try to remember what you were looking for (it's easy to go off your search when you see something interesting). Note that travel between many city pairs required changing trains - including the one you're looking for.
Easy to look that up, now that they've scanned all those Guides
Timetable World
In the steam era did Rochester MN trains went to Omaha NE via Mankato MN.
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