Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same

• US 9,694,361 B2
• Filed: 04/09/2015
• Issued: 07/04/2017
• Est. Priority Date: 04/10/2014
• Status: Active Grant

• Current Assignee: 10X Genomics Incorporated
• Original Assignee: 10X Genomics Incorporated
• Inventors: Bharadwaj, Rajiv, Mitra, Debkishore, Ness, Kevin, Masquelier, Donald, Makarewicz, Anthony, Hindson, Christopher, Hindson, Benjamin, Saxonov, Serge
• Primary Examiner(s): Bhat, Narayan
• Application Number:
  US14/682,952
• Publication Number:
  US 20150292988A1
• Time in Patent Office: 817 Days
• Field of Search: 422 681, 422502, 435 68, 4352831, 4352885, 516 7, 516 9
• CPC Class Codes: B01L 2200/0673 Handling of plugs of fluid surrounded by immiscible fluid
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2400/049 vacuum
• CPC Class Codes: B01L 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/0241 Drop counters; Drop formers making arrays for combinatorial libraries B01J19/0046; automation of dispensing for analysis G01N35/10
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/502784 specially adapted for droplet or plug flow, e.g. digital microfluidics automatic analysis using a stream of discrete samples in a tube system G01N35/08
• CPC Class Codes: G01N 2035/00237 Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1034 Transferring microquantities of liquid
• CPC Class Codes: G01N 35/085 Flow Injection Analysis

Abstract

The disclosure provides devices, systems and methods for the generation of encapsulated reagents and the partitioning of encapsulated reagents for use in subsequent analyses and/or processing, such as in the field of biological analyses and characterization.

Claims

1. A method for partitioning microcapsules, comprising:

(a) providing a microfluidic device comprising a microfluidic channel network, wherein the microfluidic channel network comprises (i) a droplet generation junction, (ii) a first channel segment fluidly connecting a source of microcapsules to the droplet generation junction, (iii) a second channel segment fluidly connecting a source of partitioning fluid to the droplet generation junction, and (iv) a third channel segment fluidly connected to the droplet generation junction and providing an outlet to the droplet generation junction; and

(b) flowing (i) an aqueous fluid comprising a suspension of microcapsules from the source of microcapsules along the first channel segment and (ii) a partitioning fluid from the source of partitioning fluid along the second channel segment into the droplet generation junction to form a population of droplets of the aqueous fluid in the partitioning fluid, wherein the population of droplets flow along the third channel segment, and wherein (1) the first channel segment has a cross-sectional dimension that provides a flow rate of the aqueous fluid or (2) the second channel segment has a cross-sectional dimension that provides a flow rate of the partitioning fluid, such that greater than 50% of droplets of the population of droplets are occupied by microcapsules from the suspension of microcapsules.

2. The method of claim 1, wherein the flow rate of the aqueous fluid or the partitioning fluid is such that greater than 75% of droplets of the population of droplets are occupied by microcapsules from the suspension of microcapsules.

3. The method of claim 2, wherein the flow rate of the aqueous fluid or the partitioning fluid is such that greater than 90% of the droplets of the population of droplets are occupied by microcapsules from the suspension of microcapsules.

4. The method of claim 1, wherein fewer than 25% of droplets of the population of droplets comprise more than one microcapsule.

5. The method of claim 4, wherein fewer than 20% of droplets of the population of droplets comprise more than one microcapsule.

6. The method of claim 5, wherein fewer than 15% of droplets of the population of droplets comprise more than one microcapsule.

7. The method of claim 6, wherein fewer than 10% of droplets of the population of droplets comprise more than one microcapsule.

8. The method of claim 7, wherein fewer than 5% of droplets of the population of droplets comprise more than one microcapsule.

9. The method of claim 1, wherein at least 80% of droplets of the population of droplets comprise a single microcapsule.

10. The method of claim 9, wherein at least 90% of droplets of the population of droplets comprise a single microcapsule.

11. The method of claim 10, wherein at least 95% of droplets of the population of droplets comprise a single microcapsule.

12. The method of claim 1, wherein (b) comprises providing one or more pressure differentials across the first and second channel segments to provide the flow rate of the aqueous fluid or the partitioning fluid.

13. The method of claim 1, wherein the microfluidic channel network further comprises one or more flow controlling structures within the first channel segment that provide the flow rate of the aqueous fluid.

14. The method of claim 1, wherein the suspension of microcapsules is a suspension of beads.

15. The method of claim 1, wherein the suspension of microcapsules is a suspension of gel microcapsules.

16. The method of claim 1, wherein a given microcapsule of the suspension of microcapsules comprises a barcode sequence.

17. The method of claim 16, wherein the barcode sequence is covalently linked to the given microcapsule.

18. The method of claim 1, wherein a given microcapsule of the suspension of microcapsules comprises a labile linkage.

19. The method of claim 18, wherein the labile linkage is a chemically cleavable linkage.

20. The method of claim 19, wherein the chemically cleavable linkage is a disulfide linkage.

21. The method of claim 1, wherein a given microcapsule of the suspension of microcapsules comprises a cross-linked polymer network.

22. The method of claim 1, wherein the aqueous fluid further comprises a reducing agent.

23. The method of claim 1, wherein the first and second channel segments have cross-sectional dimensions that provide the flow rate of the aqueous fluid and the flow rate of the partitioning fluid such that greater than 50% of droplets of the population of droplets are occupied by microcapsules from the suspension of microcapsules.

24. The method of claim 1, wherein the flow rate of the aqueous fluid or the flow rate of the partitioning fluid is such that some of the droplets of the population of droplets are unoccupied by microcapsules from the suspension of microcapsules.

25. The method of claim 24, wherein the flow rate of the aqueous fluid and the flow rate of the partitioning fluid are such that some of the droplets of the population of droplets are unoccupied by microcapsules from the suspension of microcapsules.