System and method for isolating and analyzing cells

Abstract

A system and method for isolating cells, comprising: a substrate having a broad surface; an array comprising a set of wells defined at the broad surface of the substrate, each well including: a base surface, an open surface directly opposing the base surface, defined at the broad surface of the substrate, and configured to receive one of a single cell and a single cluster of cells from a direction perpendicular to the broad surface of the substrate, and a set of channels that fluidly couple each well to at least one adjacent well; wherein the set of wells includes an interior subset and an exterior subset fluidly coupled to and surrounding the interior subset by way of the set of channels; and a fluid delivery module surrounding the array and fluidly coupled to each well in the set of wells.

We claim: 
     
         1 . A method for isolating and analyzing a population of cells in single-cell format, the method comprising:
 providing a device comprising: a substrate having a broad surface and a set of wells defined at the broad surface of the substrate, wherein each well in the set of wells comprises: a base surface defined within the substrate, and an open surface directly opposing the base surface, each well sized to receive a single target cell of the population of cells from a direction perpendicular to the broad surface of the substrate;   capturing the population of cells in single-cell format, such that each captured cell and associated cell-derived contents of the population of cells can be identified and addressed in addressable locations corresponding to the set of wells;   encapsulating cells captured at the set of wells with an encapsulation material;   delivering a set of process reagents to the set of wells, with diffusion of the set of process reagents through the encapsulation material to contents of the set of wells;   performing a set of single-cell processing operations, in-situ, upon contents of the set of wells; and   detecting optical signals from contents of the set of wells through at least one of the encapsulation material and the substrate, wherein the optical signals represent results of the set of single-cell processing operations.   
     
     
         2 . The method of  claim 1 , wherein the set of wells is arranged in a hexagonal close packed configuration. 
     
     
         3 . The method of  claim 1 , wherein the set of processing reagents comprises one or more of: a stain, a cocktail, a lysing reagent, a fixing reagent, a permeabilization reagent, a culture reagent, an immunochemistry reagent, an in-situ hybridization reagent, and a polymerase chain reaction reagent. 
     
     
         4 . The method of  claim 1 , wherein the encapsulation material comprises a polymer material with a polymerization agent. 
     
     
         5 . The method of  claim 1 , wherein the encapsulation material comprises one of: an agarose, a polyacrylamide material, a hydrogel material, and a polyethylene glycol-derived material. 
     
     
         6 . The method of  claim 1 , wherein encapsulating cells captured at the set of wells with the encapsulation material comprises permitting diffusion of the set of process reagents to the set of wells, while preventing egress of captured cells and molecules above a threshold size from the set of wells. 
     
     
         7 . The method of  claim 6 , wherein preventing egress comprises preventing egress of nucleic acid material, derived from captured target cells of the population of target cells, from the set of wells and through the encapsulation layer. 
     
     
         8 . The method of  claim 1 , wherein the set of single-cell processing operations comprises one of: immunochemistry, DNA fluorescence in-situ hybridization (FISH), and mRNA FISH. 
     
     
         9 . The method of  claim 1 , wherein the substrate is transparent, such that detecting optical signals from contents of the set of wells comprises detecting optical signals through the substrate. 
     
     
         10 . The method of  claim 1 , wherein the encapsulation layer is transparent, such that detecting optical signals from contents of the set of wells comprises detecting optical signals through the encapsulation layer. 
     
     
         11 . The method of  claim 1 , further comprising contacting the substrate with a heating element, thereby uniformly transmitting heat to contents of the set of wells through the substrate. 
     
     
         12 . The method of  claim 11 , wherein uniformly transmitting heat comprises incubating captured target cells of the population of cells within the set of wells. 
     
     
         13 . The method of  claim 1 , further comprising positioning a plate adjacent to the substrate and providing a gap between the plate and the set of wells of the substrate. 
     
     
         14 . The method of  claim 13 , wherein encapsulating cells captured at the set of wells with the encapsulation material comprises transmitting the encapsulation material in a flow state through the gap, and transitioning the encapsulation material to a set state. 
     
     
         15 . The method of  claim 1 , further comprising delivering a target cell of the population of target cells into a cell removal module, upon application of a force to contents of a well of the set of wells. 
     
     
         16 . The method of  claim 1 , wherein each of the set of wells comprises a first set of fluid channels configured for fluid exchange within the system, the method further comprising diffusing one or more of the set of process reagents through each of the set of wells by way of the first set of fluid channels. 
     
     
         17 . The method of  claim 1 , wherein the device further comprises a fluid delivery module fluidly coupled to each well of the set of wells by a set of channels, wherein each of the set of channels comprises an identical length. 
     
     
         18 . The method of  claim 1 , wherein detecting optical signals comprises detecting fluorescence-based signals resulting from reactions between one or more of the set of process reagents and contents captured at the set of wells. 
     
     
         19 . The method of  claim 1 , wherein the set of wells comprises at least 250,000 individual wells. 
     
     
         20 . The method of  claim 1 , wherein each of the set of wells has a depth of at least 25 microns.