Compositions and methods for sample processing

Abstract

This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

1 . A composition for use in nucleic acid barcoding, comprising:
 a plurality of nucleic acid barcode molecules coupled to a plurality of beads, wherein said plurality of nucleic acid barcode molecules comprise a plurality of barcode sequences that are different across said plurality of beads,   wherein a given bead of said plurality of beads comprises nucleic acid barcode molecules coupled thereto, wherein a given nucleic acid barcode molecule of said nucleic acid barcode molecules comprises a barcode sequence from said plurality of barcode sequences, wherein said barcode sequence comprises a combinatorial assembly of a first nucleic acid barcode segment and a second nucleic acid barcode segment,   wherein said first nucleic acid barcode segment is the same across said nucleic acid barcode molecules coupled to said given bead,   wherein said second nucleic acid barcode segment is the same across said nucleic acid barcode molecules coupled to said given bead.   
     
     
         2 . The composition of  claim 1 , wherein at least a subset of said nucleic acid barcode molecules is in an interior of said given bead. 
     
     
         3 . The composition of  claim 2 , wherein said at least said subset of said nucleic acid barcode molecules is coupled to said interior of said given bead. 
     
     
         4 . The composition of  claim 3 , wherein said at least said subset of said nucleic acid barcode molecules is covalently bonded to said interior of said given bead. 
     
     
         5 . The composition of  claim 3 , wherein said at least said subset of said nucleic acid barcode molecules is reversibly coupled to said interior of said given bead. 
     
     
         6 . The composition of  claim 5 , wherein said at least said subset of said nucleic acid barcode molecules is reversibly coupled to said interior of said given bead through chemical cross-linkers. 
     
     
         7 . The composition of  claim 6 , wherein said chemical cross-linkers are degradable by an acid or a reducing agent. 
     
     
         8 . The composition of  claim 5 , wherein said at least said subset of said nucleic acid barcode molecules is reversibly coupled to said interior of said given bead through disulfide bonds. 
     
     
         9 . The composition of  claim 3 , wherein (i) a first subset said nucleic acid barcode molecules is coupled to said interior of said given bead and (ii) a second subset of said nucleic acid barcode molecules is coupled to an exterior of said given bead. 
     
     
         10 . The composition of  claim 1 , wherein said given nucleic acid barcode molecule comprises a targeted primer sequence or a variable primer sequence. 
     
     
         11 . The composition of  claim 1 , wherein said nucleic acid barcode molecules comprises at least 1,000 nucleic acid barcode molecules. 
     
     
         12 . The composition of  claim 11 , wherein said nucleic acid barcode molecules comprises at least 100,000 nucleic acid barcode molecules. 
     
     
         13 . The composition of  claim 12 , wherein said nucleic acid barcode molecules comprises at least 1,000,000 nucleic acid barcode molecules. 
     
     
         14 . The composition of  claim 1 , wherein said nucleic acid barcode molecules comprise unique identifiers that are different across said nucleic acid barcode molecules. 
     
     
         15 . (canceled) 
     
     
         16 . The composition of  claim 1 , wherein said plurality of beads comprises at least 100,000 nucleic acid barcode molecules with different barcode sequences. 
     
     
         17 . The composition of  claim 16 , wherein said plurality of beads comprises at least 1,000,000 nucleic acid barcode molecules with different barcode sequences. 
     
     
         18 . The composition of  claim 1 , wherein said plurality of beads is a plurality of gel beads. 
     
     
         19 . The composition of  claim 18 , wherein gel beads of said plurality of gel beads are porous. 
     
     
         20 . The composition of  claim 18 , wherein each of said plurality of gel beads is dissolvable or disruptable. 
     
     
         21 . The composition of  claim 18 , wherein said plurality of gel beads is formed upon polymerization of molecular precursors within a plurality of droplets comprising said plurality of nucleic acid barcode molecules. 
     
     
         22 . The composition of  claim 1 , wherein said plurality of beads is uniform in size. 
     
     
         23 . The composition of  claim 1 , wherein said plurality of beads has a coefficient of variation in cross-sectional dimension of less than 30%. 
     
     
         24 . The composition of  claim 1 , wherein said given bead has a diameter less than 100 micrometers. 
     
     
         25 . The composition of  claim 24 , wherein said diameter is less than 60 micrometers. 
     
     
         26 . The composition of  claim 1 , wherein said nucleic acid barcode molecules is releasable from said given bead. 
     
     
         27 . The composition of  claim 1 , wherein said first nucleic acid barcode segment or said second nucleic acid barcode segment of said given bead is different from a corresponding segment of another bead of said plurality of beads. 
     
     
         28 . The composition of  claim 1 , wherein said first nucleic acid barcode segment or said second nucleic acid barcode segment is from 4 to 20 nucleic acid bases in length. 
     
     
         29 . The composition of  claim 1 , wherein said barcode sequence is at least 15 nucleic acid bases in length. 
     
     
         30 . (canceled) 
     
     
         31 . The composition of  claim 1 , wherein said first nucleic acid barcode segment is separated from said second nucleic acid barcode segment by a nucleic acid sequence that is the same across at least a subset of said plurality of beads. 
     
     
         32 . The composition of  claim 31 , wherein said nucleic acid sequence is at least 2 nucleic acid bases in length.