# US 2025/0085199 A1 · Methods and systems for cell and bead processing

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- Number: US 2025/0085199 A1
- Document ID: US20250085199A1
- Status: Published application
- Kind: A1
- Application number: 18/888,933
- Filed: 2024-09-18
- Published: 2025-03-13
- Earliest claimed: 2018-06-25
- Assignees: 10x Genomics, Inc.
- Applicants: 10x Genomics, Inc.
- Inventors: Christopher HINDSON; Andrew D. Price; Michael Schnall-Levin
- Web page: https://patentgrep.com/patent/US20250085199A1

## CPC

- C12M 25/16: {Particles; Beads; Granular material; Encapsulation (chemical or physical processes conducted in the presence of fluids and solid particles B01J8/00)}
- G01N 1/28: Preparing specimens for investigation {including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q}(mounting specimens on microscopic slides G02B21/34; means for supporting the objects or the materials to be analysed in electron microscopes H01J37/20 {; laboratory gas handling apparatus B01L5/00})
- C12M 25/01: {Drops}
- C12M 35/08: {Chemical, biochemical or biological means, e.g. plasma jet, co-culture}
- C12N 5/0006: {Modification of the membrane of cells, e.g. cell decoration}
- G01N 1/4077: {by other techniques involving separation of suspended solids}
- C12N 2537/10: Cross-linking
- C12M: APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; {APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS}
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

The present disclosure provides methods and systems for cell and bead processing or analysis. A method for processing a cell or bead may comprise subjecting a bead to conditions sufficient to change a first characteristic or set of characteristics (e.g., cell or bead size). Such a method may further comprise subjecting the cell or bead to conditions sufficient to change a second characteristic or set of characteristics. In some cases, crosslinks may be formed within the cell or bead.

## Claims

### Claim 1

(canceled)

### Claim 2

A method comprising:
subjecting a polymer matrix encasing a cell, a cell component, or a plurality of nucleic acid barcode molecules to conditions to reduce a volume or a diameter of the polymer matrix to yield a reduced polymer matrix encasing the cell, the cell component, or the plurality of nucleic acid barcode molecules.

### Claim 3 (depends on 2)

The method of claim 2, wherein the subjecting the polymer matrix to the conditions comprises contacting the polymer matrix with a chemical species, wherein the chemical species reduces the volume or the diameter of the polymer matrix.

### Claim 4 (depends on 3)

The method of claim 3, wherein the chemical species comprises an organic solvent.

### Claim 5 (depends on 4)

The method of claim 4, wherein the organic solvent is an acetone or an alcohol.

### Claim 6 (depends on 2)

The method of claim 2, wherein the subjecting the polymer matrix to the conditions comprises changing a temperature.

### Claim 7 (depends on 2)

The method of claim 2, wherein the polymer matrix comprises poly(N-isopropylacrylamide).

### Claim 8 (depends on 2)

The method of claim 2, wherein the method reduces the volume or the diameter by at least 6%.

### Claim 9 (depends on 2)

The method of claim 2, wherein the method reduces the volume or the diameter by at least 50%.

### Claim 10 (depends on 2)

The method of claim 2, wherein the subjecting the polymer matrix to the conditions further changes a fluidity characteristic or a rigidity characteristic of the polymer matrix.

### Claim 11 (depends on 2)

The method of claim 2, wherein the subjecting the polymer matrix to the conditions further changes a porosity of the polymer matrix.

### Claim 12 (depends on 2)

The method of claim 2, wherein the subjecting the polymer matrix to the conditions further changes a refractive index of the polymer matrix.

### Claim 13 (depends on 2)

The method of claim 2, wherein the cell, the cell component, or the plurality of nucleic acid barcode molecules is covalently attached to the polymer matrix.

### Claim 14 (depends on 2)

The method of claim 2, wherein the cell, the cell component, or the plurality of nucleic acid barcode molecules is noncovalently attached to the polymer matrix.

### Claim 15 (depends on 2)

The method of claim 2, wherein the polymer matrix comprises the cell.

### Claim 16 (depends on 15)

The method of claim 15, further comprising lysing the cell within the polymer matrix or the reduced polymer matrix.

### Claim 17 (depends on 2)

The method of claim 2, further comprising partitioning the reduced polymer matrix encasing the cell, the cell component, or the plurality of nucleic acid barcode molecules into a partition among a plurality of partitions.

### Claim 18 (depends on 17)

The method of claim 17, wherein the reduced polymer matrix encases the cell component, and wherein the partition comprises a plurality of nucleic acid barcode molecules.

### Claim 19 (depends on 18)

The method of claim 18, wherein the method further comprises using a nucleic acid barcode molecule of the plurality of nucleic acid barcode molecules and the cell component to generate a barcoded nucleic acid molecule comprising: i) a sequence of the nucleic acid barcode molecule or complement thereof, and ii) a sequence of, or associated with, the cell component.

### Claim 20 (depends on 17)

The method of claim 17, wherein the reduced polymer matrix encases the plurality of nucleic acid barcode molecules, and wherein the partition comprises a cell component.

### Claim 21 (depends on 20)

The method of claim 20, wherein the method further comprises using a nucleic acid barcode molecule of the plurality of nucleic acid barcode molecules and the cell component to generate a barcoded nucleic acid molecule comprising: i) a sequence of the nucleic acid barcode molecule or complement thereof, and ii) a sequence of, or associated with, the cell component.