Methods, systems, and devices for multiple single-cell capturing and processing using micro fluidics

Abstract

Methods, systems, and devices are described for multiple single-cell capturing and processing utilizing microfluidics. Tools and techniques are provided for capturing, partitioning, and/or manipulating individual cells from a larger population of cells along with generating genetic information and/or reactions related to each individual cell. Different capture configurations may be utilized to capture individual cells and then processing each individual cell in a multi-chamber reaction configuration. Some embodiments may provide for specific target amplification, whole genome amplification, whole transcriptome amplification, real-time PCR preparation, copy number variation, preamplification, mRNA sequencing, and/or haplotyping of the multiple individual cells that have been partitioned from the larger population of cells. Some embodiments may provide for other applications. Some embodiments may be configured for imaging the individual cells or associated reaction products as part of the processing. Reaction products may be harvested and/or further analyzed in some cases.

What is claimed is: 
     
         1 - 13 . (canceled) 
     
     
         14 . A method of analyzing a plurality of cells in a microfluidic device comprising:
 a) partitioning the plurality of cells into individual reaction partitions in the microfluidic device;   b) performing a multi-step reaction on the partitioned cells to generate reaction products; and   c) analyzing and/or processing the reaction products.   
     
     
         15 . The method of  claim 14 , wherein step (b) comprises at least one of cell lysis, RNA reverse transcription, and pre-amplification. 
     
     
         16 . The method of  claim 14 , wherein the reaction products of step (b) are both proteins and RNA. 
     
     
         17 . The method of  claim 16 , wherein the analyzing and/or processing the reaction products of step (c) comprises assaying the subcellular distribution of at least one protein. 
     
     
         18 . The method of  claim 16 , wherein the proteins are detected using antibodies. 
     
     
         19 . The method of  claim 18 , wherein the antibodies are conjugated to dyes. 
     
     
         20 . The method of  claim 14 , wherein the partitioned cells are imaged. 
     
     
         21 . The method of  claim 18 , wherein the antibodies are patterned in specific locations on the microfluidic device. 
     
     
         22 . The method of  claim 14 , wherein the multi-step reaction of step (b) is performed across multiple chambers for each cell. 
     
     
         23 . The method of  claim 14 , wherein the cells are partitioned in chambers. 
     
     
         24 . The method of  claim 14 , wherein the cells are partitioned in droplets. 
     
     
         25 . The method of  claim 16 , wherein the analyzing and/or processing the reaction products of step (c) comprises analysis of gene expression after cell lysis, RNA reverse transcription, and pre-amplification. 
     
     
         26 . The method of  claim 14 , wherein the plurality of cells comprises at least 200 cells.