Methods and systems for processing polynucleotides

Abstract

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization

1 . (canceled) 
     
     
         2 . A composition comprising:
 (i) streptavidin linked to an anchor nucleic acid molecule; and   (ii) a reporter nucleic acid molecule hybridized to the anchor nucleic acid molecule, wherein the reporter nucleic acid molecule comprises:
 (1) a barcode sequence that identifies the streptavidin or a molecule associated therewith, and 
 (2) a primer sequence, an adapter sequence, or both the primer sequence and the adapter sequence. 
   
     
     
         3 . The composition of  claim 2 , wherein the anchor nucleic acid molecule comprises a hybridization sequence and the reporter nucleic molecule comprises a reverse complement sequence of the hybridization sequence, and the anchor nucleic acid molecule hybridization sequence is hybridized to the reverse complement sequence of the hybridization sequence. 
     
     
         4 . The composition of  claim 2 , wherein the anchor nucleic acid molecule does not comprise a barcode sequence. 
     
     
         5 . The composition of  claim 2 , wherein the streptavidin is a streptavidin monomer. 
     
     
         6 . The composition of  claim 2 , wherein the streptavidin is a streptavidin tetramer. 
     
     
         7 . The composition of  claim 2 , wherein the molecule associated therewith is biotinylated. 
     
     
         8 . The composition of  claim 7 , wherein the biotinylated molecule comprises a polypeptide. 
     
     
         9 . The composition of  claim 2 , wherein the molecule configured to associate therewith is a biotinylated MHC-peptide complex. 
     
     
         10 . The composition of  claim 2 , wherein the streptavidin comprises a modified lysine amino acid residue. 
     
     
         11 . The composition of  claim 10 , wherein the anchor nucleic acid molecule is linked to the streptavidin via the modified lysine amino acid residue. 
     
     
         12 . The composition of  claim 11 , wherein the anchor nucleic acid molecule is covalently linked to the streptavidin. 
     
     
         13 . The composition of  claim 2 , wherein the barcode sequence identifies the streptavidin. 
     
     
         14 . The composition of  claim 2 , wherein the barcode sequence identifies the molecule configured to associate with the streptavidin. 
     
     
         15 . The composition of  claim 2 , wherein a plurality of the anchor nucleic acid molecules are linked to the streptavidin. 
     
     
         16 . The composition of  claim 15 , wherein a plurality of the reporter nucleic acid molecule are hybridized to the plurality of the anchor nucleic acid molecules. 
     
     
         17 . A partition comprising:
 (i) complex comprising
 (1) a streptavidin linked to an anchor nucleic acid molecule; and 
 (2) a reporter nucleic acid molecule hybridized to the anchor nucleic acid molecule, wherein the reporter nucleic acid molecule comprises a barcode sequence that identifies the streptavidin or a molecule associated therewith; 
   (ii) a cell or macromolecular constituent of a cell; and   (iii) a lysis reagent.   
     
     
         18 . The partition of  claim 17 , wherein the reporter nucleic acid molecule comprises a primer sequence, an adapter sequence, or both the primer sequence and the adapter sequence. 
     
     
         19 . The partition of  claim 17 , wherein the partition further comprises a nucleic acid barcode molecule comprising a partition barcode sequence. 
     
     
         20 . The partition of  claim 19 , wherein the nucleic acid barcode molecule comprises a capture sequence configured to couple to the adapter sequence of the reporter molecule. 
     
     
         21 . The partition of  claim 19 , wherein the nucleic acid barcode molecule is attached to a bead.