Multiplex decoding of array sensors with microspheres

1. A method of decoding an array so as to determine the location of a capture probe that has been randomly distributed on the array, said method comprising the steps of:

a) providing an array comprising a plurality of distinct capture probes, wherein said capture probes are randomly distributed on said array;

b) performing a hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal;

c) detecting the signal produced by the hybridization step at a location on said array;

d) performing a dehybridization step;

e) performing an additional hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes is different from said sets of decoder probes used in the previous hybridization step, and wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal;

f) detecting the signal produced by the additional hybridization step at said location;

g) repeating steps d-f for a number of stages sufficient to generate a code comprising the sequence of signals detected at said location, said code indicative of the capture probe present at said location; and

h) decoding said array with said code.

2. The method of claim 1 , wherein said array comprises glass or plastic.

3. The method of claim 1 , wherein said array comprises a fiber optic bundle.

4. The method of claim 1 , wherein said array comprises a flat planar surface.

5. The method of claim 4 , wherein said flat planar surface comprises a depression comprising one or more particles.

6. The method of claim 5 , wherein said capture probes are attached to said one or more particles.

7. The method of claim 6 , wherein said one or more particles comprise microspheres.

8. The method of claim 6 , wherein said one or more particles comprise beads.

9. The method of claim 4 , wherein said flat planar surface comprises at least one well having a microsphere deposited therein.

10. The method of claim 1 , wherein said capture probes and said decoder probes comprise nucleic acids.

11. The method of claim 10 , wherein said nucleic acids comprise DNA.

12. The method of claim 1 , wherein said labels comprise fluorescent labels.