Compositions and Methods for Analyte Detection

Abstract

The inventions provided herein relate to detection reagents, compositions, methods, and kits comprising the detection reagents for use in detection, identification, and/or quantification of analytes in a sample. Such detection reagents and methods described herein allow multiplexing of many more labeled species in the same procedure than conventional methods, in which multiplexing is limited by the number of available and practically usable colors.

1 .- 117 . (canceled) 
     
     
         118 . A method for identifying a protein of a biological sample, comprising:
 (a) contacting said biological sample with an antibody to permit said antibody to couple to said protein, wherein said antibody comprises at least one nucleic acid molecule coupled thereto, which nucleic acid molecule comprises a plurality of subsequences that identifies said antibody;   (b) detecting at least two subsequences of said plurality of subsequences to identify said nucleic acid molecule, thereby identifying said antibody; and   (c) using said antibody identified in (b) to identify said protein.   
     
     
         119 . The method of  claim 118 , wherein said biological sample is immobilized. 
     
     
         120 . The method of  claim 118 , wherein said biological sample is immobilized adjacent to a solid substrate or support. 
     
     
         121 . The method of  claim 118 , wherein said antibody is from a plurality of antibodies that target different proteins in said biological sample. 
     
     
         122 . The method of  claim 118 , wherein said detecting comprises sequencing by synthesis, sequencing by hybridization, or sequencing by ligation. 
     
     
         123 . The method of  claim 118 , wherein said detecting comprises sequentially hybridizing decoder probes to subsequences of said plurality of subsequences, and identifying said decoder probes. 
     
     
         124 . The method of  claim 123 , wherein each of said decoder probes comprises an optical label. 
     
     
         125 . The method of  claim 124 , wherein said optical label is a small molecule dye, a fluorescent molecule, a quantum dot, a chromophore, a chromogenic molecule, a Raman label, or any combination thereof. 
     
     
         126 . The method of  claim 118 , wherein said antibody and said at least one nucleic acid molecule are conjugated together by at least one linker. 
     
     
         127 . The method of  claim 126 , wherein said at least one linker is a bond, a linker molecule, a multivalent linker, or a particle. 
     
     
         128 . The method of  claim 118 , wherein said antibody is an antigen-binding fragment. 
     
     
         129 . The method of  claim 128 , wherein said antigen-binding fragment is a Fab, a F(ab′)2, a single-chain antibody (scFv), a single domain antibody (sdAb), or a diabody. 
     
     
         130 . The method of  claim 118 , wherein said at least one nucleic acid molecule is single-stranded, double-stranded, partially double-stranded, a hairpin, linear, circular, branched, or a concatemer. 
     
     
         131 . The method of  claim 118 , wherein subsequences of said plurality of subsequences are conjugated together by at least one sequence linker. 
     
     
         132 . The method of  claim 131 , wherein said sequence linker is a bond or a nucleotidic linker. 
     
     
         133 . The method of  claim 132 , wherein said nucleotidic linker is single-stranded, double-stranded, partially double-stranded, or a hairpin. 
     
     
         134 . The method of  claim 132 , wherein said nucleotidic linker is at least one nucleotide long. 
     
     
         135 . The method of  claim 118 , wherein said antibody comprises a plurality of nucleic acid molecules. 
     
     
         136 . The method of  claim 135 , wherein each nucleic acid molecule of said plurality of nucleic acid molecules comprises a same nucleic acid sequence. 
     
     
         137 . The method of  claim 118 , wherein said biological sample is a cell or a tissue.