Digital pcr barcoding

Abstract

Methods, compositions, and kits are provided for nucleic acid analysis, including single cell analysis.

1 - 104 . (canceled) 
     
     
         105 . A method of analyzing the nucleic acid of a plurality of cells comprising:
 providing a plurality of partitions, wherein each partition comprises:   a particle comprising a population of oligonucleotides having a barcode unique for that particle and a capture sequence; and   a sample comprising a target nucleic acid, wherein the target nucleic acid is DNA;   optionally cleaving the oligonucleotide primers conjugated to the plurality of particles from the particles;   performing (a) or (b), wherein   (a) comprises hybridizing the capture sequence, or a portion thereof, of the oligonucleotide primers to at least a portion of the target nucleic acid in each partition, and   performing template directed nucleic acid polymerization of the hybridized oligonucleotide primers, thereby covalently attaching the oligonucleotide primers to at least a portion of the target nucleic acid in each partition, wherein the template directed nucleic acid polymerization is performed before or after combining partitions; or   (b) comprises ligating the oligonucleotide primers to at least a portion of the target nucleic acid in each partition, thereby covalently attaching the oligonucleotide primers to at least a portion of the target nucleic acid in each partition, wherein the ligating is performed before combining partitions; and   combining the partitions; and   performing high throughput sequencing.   
     
     
         106 . The method of  claim 105 , comprising cleaving the oligonucleotide primers conjugated to the plurality of particles from the particles. 
     
     
         107 . The method of  claim 105 , wherein the method comprises combining partitions and then performing template directed nucleic acid polymerization of the hybridized oligonucleotide primers. 
     
     
         108 . The method of  claim 105 , wherein the method comprises performing template directed nucleic acid polymerization of the hybridized oligonucleotide primers, and then combining the partitions. 
     
     
         109 . The method of  claim 105 , wherein the sample comprising target nucleic acid comprises long fragment DNA. 
     
     
         110 . The method of  claim 105 , wherein the DNA is double stranded. 
     
     
         111 . A method of analyzing the nucleic acid of a plurality of cells comprising:
 providing a plurality of partitions, wherein each partition comprises:   a particle comprising a population of oligonucleotides having a barcode unique for that particle and a capture sequence; and   a sample comprising a target nucleic acid;   optionally cleaving the oligonucleotide primers conjugated to the plurality of particles from the particles;   hybridizing the capture sequence, or a portion thereof, of the oligonucleotide primers to at least a portion of the target nucleic acid in each partition;   combining the partitions; and then   performing template directed nucleic acid polymerization of the hybridized oligonucleotide primers, thereby covalently attaching the oligonucleotide primers to at least a portion of the target nucleic acid in each partition;   performing high throughput sequencing.   
     
     
         112 . The method of  claim 111 , comprising cleaving the oligonucleotide primers conjugated to the plurality of particles from the particles 
     
     
         113 . The method of  claim 111 , wherein the sample comprising target nucleic acid comprises a cell containing the target nucleic acid. 
     
     
         114 . The method of  claim 111 , wherein prior to the hybridizing, the cell is lysed.