A Researcher has these cubes in their lab. Cubes can always be rearranged freely within a given Lab.
The player forms a valid Run of three yellow cubes (2,3,4) and decides to use an action to Contain the yellow 3.
The yellow 3 is moved from their Lab to the empty matching space on the Containment board.
Since a yellow 3 also exists in the Primed Area, it is destroyed and removed from the game. (See Threat Phase: Prime)
The Researcher could choose to leave the remaining cubes, perhaps hoping to get a third "2" of a different color. But instead, they choose to roll the two yellow cubes used in their Run - and draws a LVL 2 Research card. (Note: The blue 2 cube cannot be rolled, as it was not part of the Run)
The rolled dice are returned to the Lab.