System and method for massively parallel analysis for nucleic acids in single cells

Abstract

Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.

What is claimed is: 
     
         1 . A library comprising at least 10,000 unique fused complexes, wherein each fused complex comprises from 5′ to 3′:
 (i) a barcode oligonucleotide affixed to a bead or a solid surface, wherein the oligonucleotide comprises a unique barcode sequence of at least six nucleotides and wherein the unique barcode sequence is selected from a pool of barcode sequences with greater than 1000-fold diversity in sequence; 
 (ii) a primer; and 
 (iii) a target nucleic acid, wherein the target nucleic acid is complementary to an RNA sequence or a DNA sequence isolated from a single cell. 
 
     
     
         2 . The library of  claim 1 , wherein the library comprises at least 25,000 unique fused complexes. 
     
     
         3 . The library of  claim 1 , wherein the library comprises at least 50,000 unique fused complexes. 
     
     
         4 . The library of  claim 3 , wherein the library comprises at least 75,000 unique fused complexes. 
     
     
         5 . The library of  claim 1 , wherein each fused complex is circular.