Devices and methods for analyzing biological samples

Abstract

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

What is claimed is: 
     
         1 . A method of processing one or more biological components of a biological sample, the method comprising:
 (a) providing a fluidic device comprising (i) a channel comprising a first surface, the biological sample, and one or more polymer precursors, wherein the one or more biological components of the biological sample are disposed on or adjacent to the first surface, (ii) a spatial energy modulating element in optical communication with the first surface, and (iii) a detector;   (b) identifying a position of the one or more biological components in the channel with the detector; and   (c) using the spatial energy modulating element to project energy into the channel such that the projected energy causes the one or more polymer precursors to form one or more polymer matrix walls of one or more chambers at least partially enclosing the one or more biological components at the position identified by the detector.   
     
     
         2 . The method of  claim 1 , wherein the biological sample comprises one or more cells. 
     
     
         3 . The method of  claim 2 , wherein a cell of the one or more cells is enclosed by a chamber of the one or more chambers. 
     
     
         4 . The method of  claim 3 , wherein the first surface comprises one or more capture elements. 
     
     
         5 . The method of  claim 4 , further comprising loading a lysing reagent into the channel, thereby lysing the cell such that one or more analytes are released from the cell, wherein at least a portion of the one or more analytes are captured by the one or more capture elements. 
     
     
         6 . The method of  claim 5 , further comprising performing one or more functional assays to assess cell viability, cell morphology, cell secretions, cell responses, intercellular interactions, or any combination thereof. 
     
     
         7 . The method of  claim 5 , wherein the one or more analytes comprise intracellular proteins. 
     
     
         8 . The method of  claim 5 , wherein the one or more analytes comprise ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and wherein the capture elements comprise capture oligonucleotides that capture the RNA or DNA. 
     
     
         9 . The method of  claim 8 , further comprising degrading the one or more polymer matrix walls of the chamber and loading the channel with a reverse transcriptase reagent to copy the RNA to produce one or more complementary DNAs, wherein the RNA comprises messenger RNA. 
     
     
         10 . The method of  claim 9 , further comprising: (a) amplifying the complementary DNA, (b) sequencing the complementary DNA, and (c) determining a transcriptome of the cell. 
     
     
         11 . The method of  claim 10 , wherein the amplifying comprises bridge amplification of the complementary DNA to form a cluster thereof, and wherein the sequencing comprises sequencing by synthesis of the complementary DNA of the cluster. 
     
     
         12 . The method of  claim 4 , wherein (i) the capture elements comprise barcodes which indicate a position thereof on the first surface, (ii) the one or more analytes comprise ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and (iii) the capture elements comprise capture oligonucleotides that capture the RNA or DNA. 
     
     
         13 . The method of  claim 12 , wherein the RNA comprises messenger RNA, and wherein the method further comprises degrading the one or more polymer matrix walls of the chamber and loading the channel with a reverse transcriptase reagent to copy the captured messenger RNAs to produce complementary DNAs. 
     
     
         14 . The method of  claim 13 , further comprising: (a) sequencing the complementary DNA, and (b) determining a transcriptome of the cell from the sequences of the complementary DNAs. 
     
     
         15 . The method of  claim 1 , wherein the biological components are disposed randomly on the first surface. 
     
     
         16 . The method of  claim 1 , wherein the channel of the fluidic device further comprises a second surface, wherein the first surface and the second surface are disposed opposite one another across the channel, and wherein the one or more polymer matrix walls of the one or more chambers extend from the first surface to the second surface to form one or more chambers each comprising an interior. 
     
     
         17 . The method of  claim 16 , wherein the interiors of a portion of the one or more chambers comprise a biological component of the one or more biological components. 
     
     
         18 . The method of  claim 16 , wherein the polymer matrix walls of the chambers have an annular-like cross-section. 
     
     
         19 . The method of  claim 18 , wherein the polymer matrix walls of the chambers have an aspect ratio of 1 or less. 
     
     
         20 . The method of  claim 1 , wherein the one or more polymer matrix walls are degradable by treatment with a degradation agent 
     
     
         21 . The method of  claim 20 , further comprising, degrading the one or more polymer matrix walls. 
     
     
         22 . The method of  claim 1 , wherein the energy projected into the channel to synthesize the one or more polymer matrix walls is light energy of a first wavelength, and wherein the one or more polymer matrix walls comprise photocleavable crosslinkers cleavable by exposure to light of a different wavelength than that of the first wavelength. 
     
     
         23 . The method of  claim 22 , wherein the photocleavable crosslinkers comprise acid labile crosslinkers, photoacid generators, or both, and wherein the degrading comprises selectively directing light to at least one of the one or more chambers to stimulate the photoacid generators therein to generate acid conditions to cleave the acid labile crosslinkers. 
     
     
         24 . The method of  claim 22 , wherein the photocleavable crosslinkers comprise base labile crosslinkers, photobase generators, or both, and wherein the degrading comprises selectively directing light to at least one of the one or more chambers to stimulate the photobase generators therein to generate basic conditions to cleave the base labile crosslinkers. 
     
     
         25 . The method of  claim 1 , wherein the detector identifies the positions of the one or more biological components from an image of light collected from the fluidic device. 
     
     
         26 . A method of analyzing one or more cells, the method comprising:
 (a) providing a fluidic device comprising (i) a channel comprising a first surface, the one or more cells, and one or more polymer precursors, wherein the one or more cells are disposed on or adjacent to the first surface, (ii) a spatial energy modulating element in optical communication with the first surface, and (iii) a detector;   (b) identifying positions of the one or more cells in the channel with the detector; and   (c) synthesizing one or more chambers in the channel separately enclosing each of the one or more cells by projecting light into the channel with the spatial energy modulating element such that the projected light causes cross-linking of the one or more polymer precursors to form polymer matrix walls of the chambers, wherein the position of each of the synthesized chambers is determined by the position of a cell enclosed thereby identified by the detector.   
     
     
         27 . The method of  claim 26 , further comprising loading into the channel a lysing reagent so that the one or more cells in the chambers are lysed and messenger ribonucleic acid (RNA) of each cell is released and captured by capture oligonucleotides in a discrete area on the first surface. 
     
     
         28 . The method of  claim 27 , further comprising degrading the one or more polymer matrix walls of the one or more chambers and loading the channel with reverse transcriptase reagents to copy the captured messenger RNAs in the discrete area to produce complementary deoxyribonucleic acids (DNAs). 
     
     
         29 . The method of  claim 28 , further comprising sequencing the complementary DNAs in the discrete areas. 
     
     
         30 . The method of  claim 28  wherein the capture oligonucleotides each comprise a barcode which indicates a position thereof on the first surface.