IP Library › Granted Patent US 12,534,760
Granted Patent B2
US 12,534,760 · App. 19/083,328 · Granted Jan 27, 2026

Methods and systems for processing polynucleotides

Inventors: Phillip Belgrader (Livermore, CA); Zachary Bent (Pleasanton, CA); Rajiv Bharadwaj (Pleasanton, CA); Vijay Kumar Sreenivasa Gopalan (Pleasanton, CA); Josephine Harada (San Francisco, CA); Christopher Hindson (Livermore, CA); Mohammad Rahimi Lenji (Pleasanton, CA); Michael Ybarra Lucero (South San Francisco, CA); Geoffrey McDermott (Livermore, CA); Elliott Meer (Pleasanton, CA); Tarjei Sigurd Mikkelsen (Dublin, CA); Christopher Joachim O'Keeffe (Pleasanton, CA); Katherine Pfeiffer (Berkeley, CA); Andrew D. Price (Hayward, CA); Paul Ryvkin (San Jose, CA); Serge Saxonov (Oakland, CA); John R. Stuelpnagel (Santa Barbara, CA); Jessica Michele Terry (Pleasanton, CA); Tobias Daniel Wheeler (Alameda, CA); Indira Wu (San Carlos, CA); Solongo Batjargal Ziraldo (San Ramon, CA); Stephane Claude Boutet (Burlingame, CA); Sarah Taylor (Pleasanton, CA); Niranjan Srinivas (Dublin, CA)
Assignee: 10X GENOMICS, INC.
C12Q1/6874C12Q1/6806C12Q1/683C12Q2525/191C12Q2537/143C12Q2563/179
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Quick Facts
Patent No.
US 12,534,760
App. No.
19/083,328
Filed
Mar 18, 2025
Granted
Jan 27, 2026
Kind
B2
Art Unit
1681
USPC
506/4
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.

Claims (32)

1 . A composition comprising:

a partition comprising a plurality of barcode molecules, wherein the plurality of barcode molecules comprises:

(a) a first barcode molecule comprising a nucleic acid barcode sequence, wherein the first barcode molecule is hybridized to a first analyte, wherein the first analyte is not messenger ribonucleic acid (mRNA) and is not hybridized to the first barcode molecule via a poly-thymine (poly-T) sequence, wherein the first analyte comprises clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or single guide ribonucleic acid (sgRNA); and

(b) a second barcode molecule comprising the nucleic acid barcode sequence, wherein the second barcode molecule is hybridized to a second analyte, wherein the second analyte is mRNA and is hybridized to the second barcode molecule via a poly-T sequence.

2 . The composition of claim 1 , wherein barcode molecules of the plurality of barcode molecules are attached to a bead.

3 . The composition of claim 2 , wherein the bead is a gel bead.

4 . The composition of claim 2 , wherein the bead comprises polyacrylamide.

5 . The composition of claim 2 , wherein barcode molecules of the plurality of barcode molecules are releasably attached to the bead.

6 . The composition of claim 1 , wherein the partition is a partition among a plurality of partitions.

7 . The composition of claim 6 , wherein the plurality of partitions comprises at least about 1,000; 5,000; 10,000; 50,000; 100,000; 500,000; 1,000,000; 5,000,000; 10,000,000; 50,000,000; 100,000,000, 500,000,000; or 1,000,000,000 partitions.

8 . The composition of claim 6 , wherein the partition is a droplet, and the plurality of partitions is a plurality of droplets.

9 . The composition of claim 6 , wherein the partition is a well, and the plurality of partitions is a plurality of wells.

10 . The composition of claim 1 , wherein the first barcode molecule and the second barcode molecule further comprise a random N-mer sequence.

11 . A composition comprising:

a plurality of droplets, wherein a droplet of the plurality of droplets comprises: a gel bead having a plurality of barcode molecules attached thereto,

wherein the plurality of barcode molecules comprises:

(a) a first barcode molecule comprising a nucleic acid barcode sequence, wherein the first barcode molecule is hybridized to a first analyte, wherein the first analyte is not mRNA and is not hybridized to the first barcode molecule via a poly-T sequence, wherein the first analyte comprises a clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or a single guide ribonucleic acid (sgRNA); and

(b) a second barcode molecule comprising the nucleic acid barcode sequence, wherein the second barcode molecule is hybridized to a second analyte, wherein the second analyte is mRNA and is hybridized to the second barcode molecule via a poly-T sequence,

wherein the first barcode molecule and the second barcode molecule further comprise a random N-mer sequence.

12 . A composition comprising:

a partition comprising a bead having a plurality of barcode molecules attached thereto, wherein the plurality of barcode molecules comprises:

(a) a first population of barcode molecules each hybridized to mRNA via poly-T sequences, wherein barcode molecules of the first population of barcode molecules each comprise a barcode sequence and a random sequence; and

(b) a second population of barcode molecules each hybridized to an analyte comprising a clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or a single guide ribonucleic acid (sgRNA) via a sequence that is not poly-T, wherein barcode molecules of the second population of barcode molecules each comprise a barcode sequence and a random sequence;

wherein barcode sequences are constant among the plurality of barcode molecules and random sequences vary among the plurality of barcode molecules.

13 . The composition of claim 12 , wherein the bead is a gel bead.

14 . The composition of claim 12 , wherein the bead comprises polyacrylamide.

15 . The composition of claim 12 , wherein the partition is a partition among a plurality of partitions.

16 . The composition of claim 15 , wherein the plurality of partitions comprises at least about 1,000; 5,000; 10,000; 50,000; 100,000; 500,000; 1,000,000: 5,000,000; 10,000,000; 50,000,000; 100,000,000, 500,000,000; or 1,000,000,000 partitions.

17 . The composition of claim 15 , wherein the partition is a droplet, and the plurality of partitions is a plurality of droplets.

18 . The composition of claim 15 , wherein the partition is a well, and the plurality of partitions is a plurality of wells.

19 . The composition of claim 11 , wherein the bead comprises polyacrylamide.

20 . The composition of claim 11 , wherein the plurality of droplets comprises at least about 1,000; 5,000; 10,000; 50,000; 100,000; 500,000; 1,000,000; 5,000,000; 10,000,000; 50,000,000; 100,000,000; 500,000,000; or 1,000,000,000 droplets.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 12, 2025
From: BELGRADER, PHILLIP; BENT, ZACHARY; BHARADWAJ, RAJIV; SREENIVASA GOPALAN, VIJAY KUMAR; HARADA, JOSEPHINE; HINDSON, CHRISTOPHER; LENJI, MOHAMMAD RAHIMI; LUCERO, MICHAEL YBARRA; MCDERMOTT, GEOFFREY; MEER, ELLIOTT; MIKKELSEN, TARJEI SIGURD; O'KEEFFE, CHRISTOPHER JOACHIM; PFEIFFER, KATHERINE; PRICE, ANDREW D.; RYVKIN, PAUL; SAXONOV, SERGE; STUELPNAGEL, JOHN R.; TERRY, JESSICA MICHELE; WHEELER, TOBIAS DANIEL; WU, INDIRA; ZIRALDO, SOLONGO BATJARGAL; BOUTET, STEPHANE CLAUDE; TAYLOR, SARAH; SRINIVAS, NIRANJAN
To: 10X GENOMICS, INC.
Reel/Frame 073535/0081 →
Continuity (14)
Continuation 18786209 · Jul 26, 2024
Continuation 17473760 · Sep 13, 2021
Continuation 17084481 · Oct 29, 2020
Continuation 16443638 · Jun 17, 2019
Continuation 16439675 · Jun 12, 2019
Continuation In Part PCTUS2018064600 · Dec 7, 2018
Continuation In Part 16107685 · Aug 21, 2018
Continuation In Part 16107685 · Aug 21, 2018
Continuation In Part 15933299 · Mar 22, 2018
Continuation 15720085 · Sep 29, 2017
Provisional Application 62723960 · Aug 28, 2018
Provisional Application 62596557 · Dec 8, 2017
Provisional Application 62438341 · Dec 22, 2016
Related Publication 20250257396A1 · Aug 14, 2025
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