Combinatorial decoding of random nucleic acid arrays

A method of determining the location of a decoding sequence on an array composition, said method comprising:

• a) providing an array composition comprising:
• i) a substrate with a surface comprising discrete sites;
• and
• ii) a population of microspheres comprising at least a first and a second subpopulation distributed on said discrete sites, wherein each subpopulation comprises identifier nucleic acid sequences comprising:
• 1) the same primer sequence;
• and
• 2) a different decoding sequence adjacent to said primer sequence;
• wherein said microspheres are distributed on said surface;
• and
• b) providing a first set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence, a variable sequence, and at least one decoding nucleotide included in said variable sequence that will basepair with at least one nucleotide of at least one of said decoding sequences, wherein said first set comprises different subsets of combinatorial decoding probes, each subset having the same decoding nucleotide and a first label specific to said same decoding nucleotide;
• and
• c) adding to said array composition a subset of said first set of combinatorial decoding probes and detecting the presence of said first label, thereby determining the location of said decoding sequence on said array composition.