Matrix runs are shadowruns in which you are asked to go into a computer system and do one of several things (download data, upload data, delete data, crash the CPU). The data transfers must be done from a specific datastore (DS) on the system, which of course the Johnson tells you about. Actually, the Johnson won't specifically refer to the actual DS's name, so if you're confused, make sure to check the CyberInfo screen in the Cyberdeck screen for a listing of the specific Node to visit and the specific action to perform.