Spatially distinguished, multiplex nucleic acid analysis of biological specimens

A method for spatially tagging target nucleic acids of a biological specimen, comprising:

• (a) providing a solid support comprising a population of nucleic acid probes attached at randomly located positions on the solid support, wherein a nucleic acid probe in the population of nucleic acid probes comprises:
• (i) a target capture sequence and (ii) a spatial tag sequence that differs from spatial tag sequences of nucleic acid probes in the population at other randomly located positions on the solid support;
• (b) performing a nucleic acid detection reaction to determine the spatial tag sequences at the randomly located positions on the solid support;
• (c) contacting the biological specimen with a portion of the population of nucleic acid probes on the solid support;
• (d) hybridizing one or more of the target capture sequences of the population of nucleic acid probes to target nucleic acids from the biological specimen that are proximal to the population of nucleic acid probes;
• and
• (e) extending the one or more target capture sequences to produce extended probes that comprise complementary sequences to the target nucleic acids, or portions thereof, and the spatial tag sequences, thereby spatially tagging the target nucleic acids of the biological specimen.