Multiplex decoding of array sensors with microspheres

Abstract

The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.

1 . A system of decoding an array, said system comprising:
 an array comprising a plurality of distinct capture probes, wherein said capture probes are randomly distributed on said array;   a plurality of first sets of decoder probes hybridized with said capture probes, wherein each of said first sets of decoder probes comprises a different label, each different label producing a different signal;   a plurality of second sets of decoder probes hybridized with said capture probes, wherein each of said second sets of decoder probes is different from said first sets of decoder probes, and wherein each of said second sets of decoder probes comprises a different label, each different label producing a different signal; and   a detector capable of detecting said different signals produced by the hybridization of said first sets of decoder probes and detecting said different signals produced by the hybridization of said second sets of decoder probes so as to generate a code indicative of the location of a capture probe, thereby decoding said array.   
     
     
         2 . The system of  claim 1 , wherein said array comprises a flat planar surface. 
     
     
         3 . The system of  claim 2 , wherein said flat planar surface comprises a depression comprising one or more particles. 
     
     
         4 . The system of  claim 3 , wherein said capture probes are attached to said one or more particles. 
     
     
         5 . The system of  claim 4 , wherein said one or more particles comprise microspheres. 
     
     
         6 . The system of  claim 2 , wherein said flat planar surface comprises at least one well having a microsphere deposited therein. 
     
     
         7 . The system of  claim 1 , wherein said capture probes and said decoder probes comprise nucleic acids. 
     
     
         8 . The system of  claim 1 , wherein said labels comprise fluorescent labels. 
     
     
         9 . (canceled) 
     
     
         10 . A method of decoding an array, said method comprising:
 contacting an array comprising a plurality of particle subpopulations, wherein each particle subpopulation comprises a distinct bioactive agent and wherein capture probes are randomly distributed on said array, with a first population of decoder probes, said first population comprising a plurality of different labels;   obtaining a first image of the location of said first population of decoder probes;   removing said first population of decoder probes;   contacting said array with a second population of decoder probes, said second population comprising a plurality of different labels;   obtaining a second image of the location of said second population of decoder probes; and   comparing said first image with said second image to determine the identity of the label that is present at a location in said first image and the identity of the label that is present at the same location in said second image so as to generate a code indicative of the location of a capture probe, thereby decoding said array.   
     
     
         11 . The method of  claim 10 , wherein the particles comprise microspheres. 
     
     
         12 . The method of  claim 10 , wherein the number of labels in said first population of decoder probes or said second population of decoder probes is less than the number of subpopulations of particles. 
     
     
         13 . The method of  claim 10 , wherein said first population of decoder probes and said second population of decoder probes comprise the same population of decoder probes, said first population of decoder probes comprising different labels than said second population of decoder probes. 
     
     
         14 . The method of  claim 10 , wherein at least one of said bioactive agents comprises a nucleic acid. 
     
     
         15 . The method of  claim 10 , wherein said first population of decoder probes and said second population of decoder probes comprise fluorescent labels. 
     
     
         16 . A method of decoding an array, said method comprising:
 providing an array comprising a population of microspheres having capture probes attached thereto, said population of microspheres being randomly distributed on said array at discrete sites;   hybridizing a plurality of first sets of decoder probes with said capture probes, wherein each of said first sets of decoder probes comprises a different label, each different label producing a different signal;   removing said plurality of first sets of decoder probes;   hybridizing a plurality of second sets of decoder probes with said capture probes, wherein each of said second sets of decoder probes comprises a different label, each different label producing a different signal; and   detecting said different signals produced by the hybridization of said first sets of decoder probes and detecting said different signals produced by the hybridization of said second sets of decoder probes so as to generate a code indicative of the location of a capture probe, thereby decoding said array.   
     
     
         17 . The method of  claim 16 , wherein said discrete sites are wells. 
     
     
         18 . The method of  claim 16 , wherein said array comprises a flat planar surface. 
     
     
         19 . The method of  claim 16 , wherein said capture probes and said decoder probes comprise nucleic acids. 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . (canceled) 
     
     
         25 . (canceled) 
     
     
         26 . (canceled)