The entrance hall of Monticello (this photo exaggerates its size, I think) was Jefferson's museum for visitors.
Many items on display came from the Lewis & Clark expedition: There were clothing, weapons, and other artifacts from the tribes of the Northern Plains and Rocky Mountains. (These are long gone, but have been re-created by Indian artisans of today.) On the natural history side of the room are antlers, fossils, and so on.
Many Americans have heard that Jefferson instructed Lewis and Clark to be on the lookout for actual live mastodons and woolly mammoths. Failing that, they were to bring back fossils.
And here is a wonderful web site about that aspect of their expedition: Lewis & Clark's Lost World: Paleontology and the Expedition.