Capsule Array Devices and Methods of Use

Abstract

This disclosure provides microwell capsule array devices. The microwell capsule array devices are generally capable of performing one or more sample preparation operations. Such sample preparation operations may be used as a prelude to one more or more analysis operations. For example, a device of this disclosure can achieve physical partitioning and discrete mixing of samples with unique molecular identifiers within a single unit in preparation for various analysis operations. The device may be useful in a variety of applications and most notably nucleic-acid-based sequencing, detection and quantification of gene expression and single-cell analysis.

What is claimed is: 
     
         1 . A method for delivering a reagent to a partition, comprising:
 providing the reagent releasably coupled to a microcapsule;   separating the microcapsule into a partition; and   releasing the reagent into the partition.   
     
     
         2 . The method of  claim 1 , wherein the releasing step comprises applying a stimulus to the microcapsule to release the reagent into the partition. 
     
     
         3 . The method of  claim 2 , wherein the stimulus is selected from a chemical stimulus, an electrical stimulus, a thermal stimulus, a magnetic stimulus, and a photostimulus. 
     
     
         4 . The method of  claim 3 , wherein the stimulus comprises a chemical stimulus. 
     
     
         5 . The method of  claim 4 , wherein the microcapsule comprises chemical cross-linking and the chemical stimulus cleaves the chemical cross-linking to release the reagent into the partition. 
     
     
         6 . The method of  claim 4 , wherein the reagent is coupled to the microcapsule through a chemically cleavable linkage, and the chemical stimulus cleaves the chemically cleavable linkage to release the reagent into the partition. 
     
     
         7 . The method of  claim 5 , wherein the chemical cross-linking comprises disulfide bonds. 
     
     
         8 . The method of  claim 7 , wherein the chemical stimulus comprises a reducing agent. 
     
     
         9 . The method of  claim 8 , wherein the reducing agent is selected from dithiothreitol and tris(2-carboxyethyl)phosphine 
     
     
         10 . The method of  claim 6 , wherein the chemically cleavable linkage comprises a disulfide bond. 
     
     
         11 . The method of  claim 10 , wherein the chemical stimulus comprises a reducing agent. 
     
     
         12 . The method of  claim 11 , wherein the reducing agent is selected from dithiothreitol and tris(2-carboxyethyl)phosphine 
     
     
         13 . The method of  claim 3 , wherein the stimulus comprises a thermal stimulus. 
     
     
         14 . The method of  claim 13 , wherein the thermal stimulus comprises heating the microcapsule to release the reagent into the partition. 
     
     
         15 . The method of  claim 1 , wherein the reagent comprises a unique identifier reagent, and the partition comprises a sample reagent to be assigned with the unique identifier reagent. 
     
     
         16 . The method of  claim 15 , wherein the unique identifier reagent comprises a nucleic acid barcode. 
     
     
         17 . The method of  claim 15 , wherein the reagent to be assigned the unique identifier reagent comprises a target nucleic acid. 
     
     
         18 . The method of  claim 16 , wherein the microcapsule comprises a population of nucleic acid barcode sequences releasably coupled thereto, wherein the barcode sequences substantially all comprise the same barcode nucleotide sequence. 
     
     
         19 . The method of  claim 10 , wherein the unique identifier reagent comprises a nucleic acid barcode, and further comprising coupling the barcode to the target nucleic acid. 
     
     
         20 . The method of  claim 1 , wherein the microcapsule comprises a crosslinked polymer microcapsule. 
     
     
         21 . The method of  claim 20 , wherein the crosslinked polymer microcapsule comprises a polyacrylamide polymer. 
     
     
         22 . The method of  claim 1 , wherein the partition is selected from a well, a microwell, and a droplet in an emulsion. 
     
     
         23 . The method of  claim 1 , comprising:
 separating a plurality of microcapsules into separate partitions, each microcapsule having a reagent releasably coupled thereto; and   releasing the reagents from the plurality of microcapsules into the different partitions.   
     
     
         24 . The method of  claim 23 , wherein the plurality of microcapsules comprises at least 1,000 microcapsules, and the releasing step comprises releasing the reagents from the at least 1000 microcapsules into separate partitions. 
     
     
         25 . The method of  claim 23 , wherein the plurality of microcapsules comprises at least 1,000 different microcapsules, each of the at least 1,000 different microcapsules comprises a different reagent, and the releasing step comprises releasing each of the different reagents into a different partition. 
     
     
         26 . The method of  claim 23 , wherein each of the at least 1000 microcapsules comprises a different reagent, and the releasing step comprises releasing a different reagent into each of at least 1000 separate partitions. 
     
     
         27 . The method of  claim 23 , wherein the plurality of microcapsules comprises at least 5,000 different microcapsules, each of the at least 5,000 different microcapsules comprises a different reagent, and the releasing step comprises releasing each of the different reagents into a different partition. 
     
     
         28 . The method of  claim 23 , wherein the plurality of microcapsules comprises at least 10,000 different microcapsules, each of the at least 10,000 different microcapsules comprises a different reagent, and the releasing step comprises releasing each of the different reagents into a different partition. 
     
     
         29 . The method of  claim 23 , wherein the plurality of microcapsules comprises at least 100,000 different microcapsules, each of the at least 100,000 different microcapsules comprises a different reagent, and the releasing step comprises releasing each of the different reagents into a different partition. 
     
     
         30 . The method of  claim 26 , wherein each different reagent comprises a different barcode sequence. 
     
     
         31 . The method of  claim 27 , wherein each different reagent comprises a different barcode sequence. 
     
     
         32 . The method of  claim 28 , wherein each different reagent comprises a different barcode sequence. 
     
     
         33 . The method of  claim 29 , wherein each different reagent comprises a different barcode sequence. 
     
     
         34 . The method of  claim 23 , wherein the reagent coupled to each of the plurality of microcapsules comprises at least 10,000 nucleic acid barcodes having the same barcode sequence releasably coupled thereto. 
     
     
         35 . The method of  claim 23 , wherein the reagent coupled to each of the plurality of microcapsules comprises at least 100,000 nucleic acid barcodes having the same barcode sequence releasably coupled thereto. 
     
     
         36 . The method of  claim 23 , wherein the reagent coupled to each of the plurality of microcapsules comprises at least 1,000,000 nucleic acid barcodes having the same barcode sequence releasably coupled thereto.