# US 10,480,028 B2 · Methods and systems for processing polynucleotides > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 10,480,028 B2 - Document ID: US10480028B2 - Status: Granted - Kind: B2 - Application number: 15/847,752 - Filed: 2017-12-19 - Published: 2018-04-26 - Granted: 2019-11-19 - Earliest claimed: 2014-06-26 - Assignees: 10x Genomics, Inc. - Applicants: 10X Genomics, Inc. - Inventors: Benjamin Hindson; Christopher Hindson; Michael Schnall-Levin; Kevin Ness; Mirna Jarosz; Serge Saxonov - Web page: https://patentgrep.com/patent/US10480028B2 ## CPC - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - C12Q 1/6804: Nucleic acid analysis using immunogens (immunoassay G01N33/53) - C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) - C12Q 1/683: involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP] - C12Q 2525/191: incorporating an adaptor - C12Q 2535/122: Massive parallel sequencing - C12Q 2537/143: Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis - C12Q 2537/149: Sequential reactions - C12Q 2563/149: Particles, e.g. beads - C12Q 2563/159: Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components - C12Q 2563/179: the label being a nucleic acid - C12Q 2565/629: being a microfluidic device - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. ## Claims ### Claim 1 A method for analyzing cells comprising: (a) contacting a plurality of cells with an antibody to provide a cell bound to said antibody, wherein said antibody is attached to a reporter oligonucleotide comprising a reporter sequence; (b) co-partitioning at least a subset of said plurality of cells into a plurality of wells, wherein a well of said plurality of wells comprises (i) said cell bound to said antibody and (ii) a first nucleic acid molecule comprising a barcode sequence; and (c) using said reporter oligonucleotide and said first nucleic acid molecule to generate a second nucleic acid molecule comprising (i) said reporter sequence, and (ii) said barcode sequence. ### Claim 2 (depends on 1) The method of claim 1, further comprising sequencing said second nucleic acid molecule or a derivative thereof to identify said reporter sequence and said barcode sequence. ### Claim 3 (depends on 1) The method of claim 1, wherein (c) comprises hybridizing said reporter oligonucleotide to said first nucleic acid molecule and performing a nucleic acid extension reaction to generate said second nucleic acid molecule. ### Claim 4 (depends on 1) The method of claim 1, wherein (c) is performed in said well of said plurality of wells. ### Claim 5 (depends on 1) The method of claim 1, wherein said first nucleic acid molecule is attached to a bead and wherein, in (b), said well comprises (i) said cell bound to said antibody and (ii) said bead. ### Claim 6 (depends on 5) The method of claim 5, wherein (c) comprises (i) hybridizing said reporter oligonucleotide to said first nucleic acid molecule to provide said bead comprising said reporter oligonucleotide attached thereto; and (ii) performing a nucleic acid extension reaction to generate said second nucleic acid molecule. ### Claim 7 (depends on 6) The method of claim 6, wherein, prior to said nucleic acid extension reaction, said bead comprising said reporter oligonucleotide attached thereto is removed from said well. ### Claim 8 (depends on 6) The method of claim 6, wherein said bead is a magnetic bead. ### Claim 9 (depends on 8) The method of claim 8, wherein, prior to said nucleic acid extension reaction, said magnetic bead comprising said reporter oligonucleotide attached thereto is removed from said well. ### Claim 10 (depends on 9) The method of claim 9, wherein said magnetic bead is removed using a magnetic field. ### Claim 11 (depends on 1) The method of claim 1, wherein said first nucleic acid molecule comprises a sequence complementary to a sequence of said reporter oligonucleotide. ### Claim 12 (depends on 1) The method of claim 1, wherein said first nucleic acid molecule comprises a unique molecular sequence. ### Claim 13 (depends on 1) The method of claim 1, wherein said first nucleic acid molecule comprises a primer sequence. ### Claim 14 (depends on 13) The method of claim 13, wherein said primer sequence is a sequencing primer sequence. ### Claim 15 (depends on 1) The method of claim 1, wherein said reporter oligonucleotide comprises a primer sequence. ### Claim 16 (depends on 15) The method of claim 15, wherein said primer sequence is a sequencing primer sequence. ### Claim 17 (depends on 1) The method of claim 1, wherein said reporter oligonucleotide comprises an adapter sequence configured to permit attachment to a flow cell of a sequencer. ### Claim 18 (depends on 1) The method of claim 1, further comprising subjecting said second nucleic acid molecule or a derivative thereof to a nucleic acid amplification reaction. ### Claim 19 (depends on 1) The method of claim 1, further comprising adding one or more functional sequences to said second nucleic acid molecule or a derivative thereof, wherein said one or more functional sequences are configured to permit attachment to a flow cell of a sequencer. ### Claim 20 (depends on 5) The method of claim 5 wherein (b) comprises co-partitioning at least said subset of said plurality of cells and a plurality of beads into said plurality of wells to provide said well comprising (i) said cell attached to said antibody and (ii) said bead. ### Claim 21 (depends on 1) The method of claim 1, wherein (b) comprises co-partitioning at least said subset of said plurality of cells and a plurality of nucleic acid barcode molecules into said plurality of wells to provide said well comprising (i) said cell bound to said antibody and (ii) said first nucleic acid molecule. ### Claim 22 (depends on 1) The method of claim 1, wherein said plurality of cells comprises 100 cells. ### Claim 23 (depends on 1) The method of claim 1, wherein said plurality of cells comprises 1,000 cells. ### Claim 24 (depends on 1) The method of claim 1, wherein said plurality of cells comprises 10,000 cells. ### Claim 25 (depends on 1) The method of claim 1, wherein said reporter sequence is complementary to said sequence of said reporter oligonucleotide. ### Claim 26 A method for analyzing cells comprising: (a) contacting a first plurality of cells with a first antibody to provide a first cell bound to said first antibody, wherein said first antibody is attached to a first reporter oligonucleotide comprising a first reporter sequence; (b) contacting a second plurality of cells with a second antibody to provide a second cell bound to said second antibody, wherein said second antibody is attached to a second reporter oligonucleotide comprising a second reporter sequence, wherein said first reporter sequence is different than said second reporter sequence; (c) pooling at least a subset of said first plurality of cells and at least a subset of said second plurality of cells to provide a pooled plurality of cells; (d) co-partitioning at least a subset of said pooled plurality of cells into a plurality of wells to provide (i) a first well comprising said first cell bound to said first antibody and a first nucleic acid molecule comprising a first barcode sequence; and (ii) a second well comprising said second cell bound to said second antibody and a second nucleic acid molecule comprising a second barcode sequence; and (e) generating (i) a third nucleic acid molecule comprising said first reporter sequence and said first barcode sequence; and (ii) a fourth nucleic acid molecule comprising said second reporter sequence and said second barcode sequence. ### Claim 27 (depends on 26) The method of claim 26, further comprising (f) sequencing (i) said third nucleic acid molecule or a derivative thereof to identify said first reporter sequence and said first barcode sequence and (ii) said fourth nucleic acid molecule or a derivative thereof to identify said second reporter sequence and said second barcode sequence; and (g) using (i) said first reporter sequence and said first barcode sequence to identify said first cell of said first plurality of cells; and (ii) said second reporter sequence and said second barcode sequence to identify said second cell of said second plurality of cells. ### Claim 28 (depends on 26) The method of claim 26, wherein said first reporter oligonucleotide is complementary to said first nucleic acid molecule or said second reporter oligonucleotide is complementary to said second nucleic acid molecule. ### Claim 29 A method for analyzing cells comprising: (a) providing a microwell array comprising a plurality of microwells; (b) providing a plurality of cells, wherein a cell of the plurality of cells is bound to an antibody attached to a reporter oligonucleotide comprising a reporter sequence; (c) providing a plurality of beads, wherein a bead of the plurality of beads comprises a barcode sequence that differs across the plurality of beads; (d) co-partitioning said plurality of cells and said plurality of beads into said microwell array, wherein a microwell of said plurality of microwells comprises (i) said cell bound to said antibody and (ii) said bead; and (e) using said reporter oligonucleotide and said bead to generate a sequencing library. ### Claim 30 (depends on 1) The method of claim 1, wherein (a) comprises contacting said plurality of cells with a plurality of antibodies comprising a plurality of reporter oligonucleotides, wherein a given antibody of said plurality of antibodies is attached to a given reporter oligonucleotide of said plurality of reporter oligonucleotides and wherein said given reporter oligonucleotide comprises a given reporter sequence that identifies said given antibody. ### Claim 31 (depends on 30) The method of claim 30, wherein, in (b), said microwell comprises (i) said cell bound to at least a subset of said plurality of antibodies, including said given antibody; and (ii) a plurality of nucleic acid barcode molecules, including said first nucleic acid molecule; wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a common barcode sequence. ### Claim 32 (depends on 31) The method of claim 31, wherein (c) comprises generating a plurality of barcoded nucleic acid molecules, including said second nucleic acid molecule, and wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises (i) said given reporter sequence corresponding to said given antibody of said subset of said plurality of antibodies; and (ii) said common barcode sequence. ### Claim 33 (depends on 32) The method of claim 32, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 34 (depends on 33) The method of claim 33, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises said unique molecular sequence. ### Claim 35 (depends on 34) The method of claim 34, further comprising sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof to measure the quantity of a protein in said cell. ### Claim 36 (depends on 6) The method of claim 6, wherein said reporter oligonucleotide comprises a poly-A sequence, said first nucleic acid molecule comprises a poly-T sequence, and said hybridizing occurs via hybridization between said poly-A sequence and said poly-T sequence. ### Claim 37 (depends on 34) The method of claim 34, further comprising (d) using a messenger ribonucleic acid RNA (mRNA) of said cell and a third nucleic acid molecule comprising said barcode sequence to generate a fourth nucleic acid molecule comprising (i) a sequence corresponding to said mRNA and (ii) said barcode sequence; wherein said third nucleic acid molecule comprises a poly-T sequence, and wherein (d) comprises hybridizing a poly-A sequence of said mRNA to said poly-T sequence. ### Claim 38 (depends on 37) The method of claim 37, further comprising sequencing said fourth nucleic acid molecule or a derivative thereof to identify said sequence corresponding to said mRNA and said barcode sequence. ### Claim 39 (depends on 32) The method of claim 32, wherein each reporter oligonucleotide of said plurality of reporter oligonucleotides comprises a poly-A sequence, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a poly-T sequence, and wherein (c) comprises (i) hybridizing reporter oligonucleotides of said plurality of reporter oligonucleotides to nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules; and (ii) performing a nucleic acid extension reaction to generate said plurality of barcoded nucleic acid molecules. ### Claim 40 (depends on 39) The method of claim 39, further comprising (d) hybridizing a poly-A sequence of a plurality of messenger RNA (mRNA) molecules of said cell to said poly-T sequence of nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules and performing a reverse transcription reaction to generate a plurality of barcoded complementary deoxyribonucleic acid (cDNA) molecules, wherein each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises (i) a sequence corresponding to a mRNA molecule of said plurality of mRNA molecules and (ii) said common barcode sequence. ### Claim 41 (depends on 40) The method of claim 40, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 42 (depends on 41) The method of claim 41, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules and each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises said unique molecular sequence. ### Claim 43 (depends on 42) The method of claim 42, further comprising (i) sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof; (ii) sequencing said plurality of barcoded cDNA molecules or a derivative thereof; and (iii) using said unique molecular sequence to measure a quantity of a protein or a quantity of a mRNA in said cell. ### Claim 44 (depends on 1) The method of claim 1, wherein said plurality of nucleic acid barcode molecules are attached to a bead and wherein said microwell comprises said bead. ### Claim 45 (depends on 40) The method of claim 40, wherein said plurality of nucleic acid barcode molecules are attached to a bead and wherein said microwell comprises said bead. ### Claim 46 (depends on 1) The method of claim 1, wherein said antibody binds to a cell surface feature of said cell. ### Claim 47 (depends on 1) The method of claim 1, wherein said antibody binds to a protein of said cell. ### Claim 48 (depends on 47) The method of claim 47, wherein said protein comprises a cell surface protein. ### Claim 49 (depends on 47) The method of claim 47, wherein said protein comprises an intracellular protein. ### Claim 50 (depends on 48) The method of claim 48, wherein said cell surface protein is a cluster of differentiation (CD) protein. ### Claim 51 (depends on 30) The method of claim 30, wherein each antibody of said plurality of antibodies that has a binding affinity for a common antigen comprises a common reporter sequence. ### Claim 52 (depends on 51) The method of claim 51, wherein each antibody of said plurality of antibodies that has a binding affinity for a different antigen comprises a different reporter sequence. ### Claim 53 (depends on 30) The method of claim 30, wherein different antibodies are attached to reporter oligonucleotides having different reporter sequences corresponding to said different antibodies. ### Claim 54 (depends on 26) The method of claim 26, wherein (a) comprises contacting said first plurality of cells with a plurality of antibodies comprising a plurality of reporter oligonucleotides, wherein each antibody of said plurality of antibodies is attached to a reporter oligonucleotide comprising a reporter sequence. ### Claim 55 (depends on 54) The method of claim 54, wherein, in (d), said first well comprises (i) said first cell bound to at least a subset of said plurality of antibodies, including said first antibody, and (ii) a plurality of nucleic acid barcode molecules, including said first nucleic acid molecule; wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a common barcode sequence. ### Claim 56 (depends on 55) The method of claim 55, wherein (e) comprises generating a plurality of barcoded nucleic acid molecules, including said third nucleic acid molecule, and wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises (i) a reporter sequence corresponding to an antibody of said subset of said plurality of antibodies; and (ii) said common barcode sequence. ### Claim 57 (depends on 56) The method of claim 56, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 58 (depends on 57) The method of claim 57, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises said unique molecular sequence. ### Claim 59 (depends on 58) The method of claim 58, further comprising sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof to measure the quantity of a protein in said first cell. ### Claim 60 (depends on 27) The method of claim 27, wherein said first nucleic acid molecule is attached to a bead and wherein, in (d), said first well comprises (i) said first cell bound to said first antibody and (ii) said bead. ### Claim 61 (depends on 60) The method of claim 60, wherein said first reporter oligonucleotide comprises a poly-A sequence, wherein said first nucleic acid molecule comprises a poly-T sequence, and wherein (g) comprises (i) hybridizing said poly-A sequence of said first reporter oligonucleotide to said poly-T sequence of said first nucleic acid molecule to provide said bead comprising said first reporter oligonucleotide attached thereto, and (ii) performing a nucleic acid extension reaction to generate said third nucleic acid molecule. ### Claim 62 (depends on 61) The method of claim 61, further comprising (h) using a messenger ribonucleic acid RNA (mRNA) of said first cell and a fifth nucleic acid molecule comprising said first barcode sequence to generate a sixth nucleic acid molecule comprising (i) a sequence corresponding to said mRNA and (ii) said first barcode sequence; wherein said fifth nucleic acid molecule comprises a poly-T sequence, and wherein (h) comprises hybridizing a poly-A sequence of said mRNA to said poly-T sequence. ### Claim 63 (depends on 62) The method of claim 62, further comprising sequencing said sixth nucleic acid molecule or a derivative thereof to identify said sequence corresponding to said mRNA and said first barcode sequence. ### Claim 64 (depends on 56) The method of claim 56, wherein each reporter oligonucleotide of said plurality of reporter oligonucleotides comprises a poly-A sequence, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a poly-T sequence, and wherein (e) comprises (i) hybridizing reporter oligonucleotides of said plurality of reporter oligonucleotides to nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules; and (ii) performing a nucleic acid extension reaction to generate said plurality of barcoded nucleic acid molecules. ### Claim 65 (depends on 64) The method of claim 64, further comprising (f) hybridizing a poly-A sequence of a plurality of messenger RNA (mRNA) molecules of said first cell to said poly-T sequence of nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules to generate a plurality of barcoded complementary deoxyribonucleic acid (cDNA) molecules, wherein each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises (i) a sequence corresponding to a mRNA molecule of said plurality of mRNA molecules and (ii) said common barcode sequence. ### Claim 66 (depends on 65) The method of claim 65, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 67 (depends on 66) The method of claim 66, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules and each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises said unique molecular sequence. ### Claim 68 (depends on 67) The method of claim 67, further comprising (i) sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof; (ii) sequencing said plurality of barcoded cDNA molecules or a derivative thereof; and (iii) using said unique molecular sequence to measure a quantity of a protein or a quantity of a mRNA in said first cell. ### Claim 69 (depends on 55) The method of claim 55, wherein said plurality of nucleic acid barcode molecules are attached to a bead and wherein said first well comprises said bead. ### Claim 70 (depends on 65) The method of claim 65, wherein said plurality of nucleic acid barcode molecules are attached to a bead and wherein said first well comprises said bead. ### Claim 71 (depends on 26) The method of claim 26, wherein said first antibody binds to a cell surface feature of said first cell. ### Claim 72 (depends on 26) The method of claim 26, wherein said first antibody binds to a protein of said first cell. ### Claim 73 (depends on 72) The method of claim 72, wherein said protein comprises a cell surface protein. ### Claim 74 (depends on 72) The method of claim 72, wherein said protein comprises an intracellular protein. ### Claim 75 (depends on 73) The method of claim 73, wherein said cell surface protein is a cluster of differentiation (CD) protein. ### Claim 76 (depends on 72) The method of claim 72, wherein each antibody of said plurality of antibodies that has a binding affinity for a common antigen comprises a common reporter sequence. ### Claim 77 (depends on 76) The method of claim 76, wherein each antibody of said plurality of antibodies that has a binding affinity for a different antigen comprises a different reporter sequence. ### Claim 78 (depends on 54) The method of claim 54, wherein different antibodies are attached to reporter oligonucleotides having different reporter sequences corresponding to said different. ### Claim 79 (depends on 29) The method of claim 29, wherein, in (b), said cell is bound to at least a subset of a plurality of antibodies comprising a plurality of reporter oligonucleotides, including said antibody, and wherein each antibody of said plurality of antibodies is attached to a given reporter oligonucleotide comprising a given reporter sequence. ### Claim 80 (depends on 79) The method of claim 79, wherein, in (d), said microwell comprises (i) said cell bound to said at least said subset of said plurality of antibodies, including said antibody; and (ii) said bead, wherein said bead comprises a plurality of nucleic acid barcode molecules; wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a common barcode sequence. ### Claim 81 (depends on 80) The method of claim 80, wherein (e) comprises generating a plurality of barcoded nucleic acid molecules, and wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises (i) said given reporter sequence corresponding to a given antibody of said subset of said plurality of antibodies; and (ii) said common barcode sequence. ### Claim 82 (depends on 81) The method of claim 81, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 83 (depends on 82) The method of claim 82, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises said unique molecular sequence. ### Claim 84 (depends on 83) The method of claim 83, further comprising sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof to measure the quantity of a protein in said cell. ### Claim 85 (depends on 29) The method of claim 29, wherein said reporter oligonucleotide comprises a poly-A sequence, wherein a first nucleic acid molecule is attached to said bead, wherein said first nucleic acid molecule comprises a poly-T sequence and said barcode sequence, and wherein (e) comprises (i) hybridizing said poly-A sequence of said reporter oligonucleotide to said poly-T sequence of said first nucleic acid molecule attached to said bead, to provide said bead comprising said reporter oligonucleotide attached thereto, and (ii) performing a nucleic acid extension reaction to generate a barcoded nucleic acid molecule. ### Claim 86 (depends on 85) The method of claim 85, wherein a second nucleic acid molecule is attached to said bead, wherein said second nucleic acid molecule comprises a poly-T sequence and said barcode sequence, and further comprising (f) hybridizing a poly-A sequence of a messenger ribonucleic acid RNA (mRNA) of said cell to said poly-T sequence of said second nucleic acid molecule to provide said bead comprising said mRNA attached thereto; and (g) generating a third nucleic acid molecule comprising (i) a sequence corresponding to said mRNA and (ii) said barcode sequence. ### Claim 87 (depends on 86) The method of claim 86, further comprising sequencing said third nucleic acid molecule or a derivative thereof to identify said sequence corresponding to said mRNA and said barcode sequence. ### Claim 88 (depends on 81) The method of claim 81, wherein each reporter oligonucleotide of said plurality of reporter oligonucleotides comprises a poly-A sequence, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a poly-T sequence, and wherein (e) comprises (i) hybridizing reporter oligonucleotides of said plurality of reporter oligonucleotides to nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules; and (ii) performing a nucleic acid extension reaction to generate said plurality of barcoded nucleic acid molecules. ### Claim 89 (depends on 88) The method of claim 88, further comprising (f) hybridizing a poly-A sequence of a plurality of messenger RNA (mRNA) molecules of said cell to said poly-T sequence of nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules and performing a reverse transcription reaction to generate a plurality of barcoded complementary deoxyribonucleic acid (cDNA) molecules, wherein each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises (i) a sequence corresponding to a mRNA molecule of said plurality of mRNA molecules and (ii) said common barcode sequence. ### Claim 90 (depends on 89) The method of claim 89, wherein each nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a unique molecular sequence. ### Claim 91 (depends on 90) The method of claim 90, wherein each barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules and each barcoded cDNA molecule of said plurality of barcoded cDNA molecules comprises said unique molecular sequence. ### Claim 92 (depends on 91) The method of claim 91, further comprising (i) sequencing said plurality of barcoded nucleic acid molecules or a derivative thereof; (ii) sequencing said plurality of barcoded cDNA molecules or a derivative thereof; and (iii) using said unique molecular sequence to measure the quantity of a protein or the quantity of a mRNA in said cell. ### Claim 93 (depends on 29) The method of claim 29, wherein said antibody binds to a cell surface feature of said cell. ### Claim 94 (depends on 29) The method of claim 29, wherein said antibody binds to a protein of said cell. ### Claim 95 (depends on 94) The method of claim 94, wherein said protein comprises a cell surface protein. ### Claim 96 (depends on 94) The method of claim 94, wherein said protein comprises an intracellular protein. ### Claim 97 (depends on 95) The method of claim 95, wherein said cell surface protein is a cluster of differentiation (CD) protein. ### Claim 98 (depends on 79) The method of claim 79, wherein each antibody of said plurality of antibodies that has a binding affinity for a common antigen comprises a common reporter sequence. ### Claim 99 (depends on 98) The method of claim 98, wherein each antibody of said plurality of antibodies that has a binding affinity for a different antigen comprises a different reporter sequence. ### Claim 100 (depends on 79) The method of claim 79, wherein different antibodies are attached to reporter oligonucleotides having different reporter sequences corresponding to said different antibodies.