Spatially Encoded Biological Assays

Abstract

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

1 . (canceled) 
     
     
         2 . A substrate comprising (i) a capture agent that binds specifically to a target biological molecule and (ii) a coding identifier, wherein each of the capture agent and the coding identifier are independently attached to a location on a surface of the substrate. 
     
     
         3 . The substrate of  claim 2 , wherein the capture agent is attached to the surface of the substrate by a chemical-coupling mechanism. 
     
     
         4 . The substrate of  claim 2 , wherein the capture agent is attached to the surface of the substrate through ligation. 
     
     
         5 . The substrate of  claim 2 , wherein the capture agent is attached to the surface of the substrate through photolithographic immobilization methods. 
     
     
         6 . The substrate of  claim 2 , wherein the coding identifier is attached to the surface of the substrate through a chemical-coupling mechanism. 
     
     
         7 . The substrate of  claim 2 , wherein the coding identifier is attached to the surface of the substrate through ligation. 
     
     
         8 . The substrate of  claim 2 , wherein the coding identifier is attached to the surface of the substrate through photolithographic immobilization methods. 
     
     
         9 . The substrate of  claim 2 , the capture agent is a nucleic acid. 
     
     
         10 . The substrate of  claim 2 , wherein the capture agent is a protein. 
     
     
         11 . The substrate of  claim 10 , wherein the protein is an antibody. 
     
     
         12 . The substrate of  claim 2 , wherein the capture agent is a small molecule. 
     
     
         13 . The substrate of  claim 2 , wherein the capture agent is a substrate for an enzyme. 
     
     
         14 . The substrate of  claim 2 , wherein the target biological molecule comprises a nucleic acid. 
     
     
         15 . The substrate of  claim 14 , wherein the nucleic acid comprises a single nucleotide polymorphism. 
     
     
         16 . The substrate of  claim 14 , wherein the nucleic acid comprises a mutation. 
     
     
         17 . The substrate of  claim 14 , wherein the nucleic acid is genomic DNA. 
     
     
         18 . The substrate of  claim 14 , wherein the nucleic acid is mRNA. 
     
     
         19 . The substrate of  claim 9 , wherein the nucleic acid comprises a universal sequence. 
     
     
         20 . The substrate of  claim 9 , wherein the nucleic acid is a gene-specific sequence. 
     
     
         21 . The substrate of  claim 2 , wherein the substrate comprises a slide. 
     
     
         22 . The substrate of  claim 2 , wherein the substrate comprises a flow-cell. 
     
     
         23 . The substrate of  claim 2 , wherein the substrate comprises a bead. 
     
     
         24 . The substrate of  claim 2 , wherein the target biological molecule comprises a protein. 
     
     
         25 . The substrate of  claim 2 , wherein the capture agent comprises a protein conjugated to an oligonucleotide comprising a nucleic acid sequence and wherein the protein specifically binds to the target biological molecule. 
     
     
         26 . The substrate of  claim 2 , wherein the capture agent binds specifically to a target biological molecule of a tissue sample. 
     
     
         27 . The substrate of  claim 2 , wherein the capture agent further comprises a first primer binding region. 
     
     
         28 . The substrate of  claim 2 , wherein the coding identifier further comprises a second primer binding region. 
     
     
         29 . The substrate of  claim 2 , wherein the substrate further comprises a cleavable site. 
     
     
         30 . The substrate of  claim 2 , wherein the coding identifier is configured to identify the location of the coding identifier on the surface of the substrate. 
     
     
         31 . The substrate of  claim 2 , further comprising a fiducial marker.