Methods and compositions for analyzing cellular components

Abstract

Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitiating nucleic acid, proteins, organelles, and/or cellular metabolites.

1 - 102 . (canceled) 
     
     
         103 . A method of analyzing one or more analytes of a plurality of contiguity preserving elements (CEs), the method comprising:
 (a) providing a plurality of CEs, wherein the CE are physical entities that preserve analytes in close proximity;   (b) compartmentalizing the CEs into a plurality of first compartments, wherein each compartment comprises multiple CEs;   (c) providing a set of first reporter moieties to an analyte of each CE in each of the plurality of first compartments, wherein each first reporter moiety in the set of first reporter moieties provided to the analyte of each first compartment is different from the first reporter moieties provided to the analyte of each of the other first compartments;   (d) combining the CEs comprising the first reporter moieties;   (e) splitting the CEs comprising the first reporter moieties into a plurality of second compartments;   (f) providing a set of second reporter moieties to the analyte of each CE in each of the plurality of second compartments, wherein each second reporter moiety in the set of second reporter moieties provided to the analyte of each second compartment is different from the second reporter moieties provided to the analyte of each of the other second compartments;   (g) combining the CEs comprising the first and second reporter moieties;   (h) analyzing the analytes comprising the reporter moieties of each compartment,   wherein such analysis detects a single cell which is the source of each analyte.   
     
     
         104 . The method of  claim 103 , wherein the CE is a cell, an embedded cell, or a preserved cell. 
     
     
         105 . The method of  claim 103 , wherein each compartment of step (e) comprises multiple CEs. 
     
     
         106 . The method of  claim 103 , wherein the analyte comprises nucleic acid and the first reporter moiety is introduced through tagmentation, ligation, or PCR. 
     
     
         107 . The method of  claim 103 , wherein the analyte comprises nucleic acid and the first reporter moiety is introduced through transcribing RNA to cDNA. 
     
     
         108 . The method of  claim 103 , wherein the analyte comprises nucleic acid and the second reporter moiety is introduced through tagmentation, ligation, or PCR. 
     
     
         109 . The method of  claim 103 , wherein the first reporter moiety comprises a nucleic acid barcode. 
     
     
         110 . The method of  claim 103 , wherein the second reporter moiety comprises a nucleic acid barcode. 
     
     
         111 . The method of  claim 103 , wherein the method further comprises, prior to step (h): splitting the CEs comprising the first and second reporter moieties into a plurality of third compartments; providing a set of third reporter moieties to the analyte of each CE in each of the plurality of third compartments, wherein each third reporter moiety in the set of third reporter moieties provided to the analyte of each third compartment is different from the third reporter moieties provided to the analyte of each of the other third compartments; and combining the CEs comprising the first, second, and third reporter moieties. 
     
     
         112 . The method of  claim 111 , wherein the analyte comprises nucleic acid and the third reporter moiety is introduced through tagmentation, ligation, or PCR. 
     
     
         113 . The method of  claim 111 , wherein the third reporter moiety comprises a nucleic acid barcode. 
     
     
         114 . The method of  claim 103 , wherein steps (b)-(g) are repeated with one or more sets of additional reporter moieties. 
     
     
         115 . The method of  claim 103 , wherein the analyte comprises DNA, RNA, or cDNA. 
     
     
         116 . The method of  claim 115 , wherein the DNA comprises genomic DNA. 
     
     
         117 . The method of  claim 103 , wherein the first reporter moieties are used to identify a sample source for each single cell. 
     
     
         118 . The method of  claim 103 , wherein detection of the analytes from the same CE are done simultaneously. 
     
     
         119 . A composition comprising a plurality of compartments, each compartment comprising a plurality of CEs,
 wherein each CE comprises an analyte that comprises a first reporter moiety and a second reporter moiety,   wherein the analyte of substantially all CEs comprise the first reporter moiety and the second reporter moiety in a unique combination, a unique position, or a combination thereof.   
     
     
         120 . The composition of  claim 119 , wherein each CE comprises the first reporter moiety and the second reporter moiety in a unique combination, a unique position, or a combination thereof. 
     
     
         121 . The composition of  claim 119 , wherein the compartments comprise a three-dimensional solid support. 
     
     
         122 . The composition of  claim 121 , wherein the three-dimensional solid support comprises a multi-well plate. 
     
     
         123 . The composition of  claim 119 , wherein the CE is a cell, embedded cell, or a preserved cell. 
     
     
         124 . The composition of  claim 119 , wherein the analyte comprises nucleic acid. 
     
     
         125 . The composition of  claim 124 , wherein the analyte comprises DNA, RNA, or cDNA. 
     
     
         126 . The composition of  claim 125 , wherein the DNA comprises genomic DNA. 
     
     
         127 . The composition of  claim 119 , wherein the first reporter moiety comprises a nucleic acid barcode. 
     
     
         128 . The composition of  claim 119 , wherein the second reporter moiety comprises a nucleic acid barcode. 
     
     
         129 . The composition of  claim 119 , wherein the plurality of CEs comprises at least 100,000 CE. 
     
     
         130 . The composition of  claim 119 , wherein the plurality of CEs comprises at least 1,000,000 CE. 
     
     
         131 . The composition of  claim 119 , wherein the CEs comprise additional sets of reporter moieties,
 wherein the analyte of each CE comprises the first reporter moiety, the second reporter moiety, and the additional sets of reporter moieties in a unique combination, a unique position, or a combination thereof.