Methods and systems for microfluidic screening

Abstract

Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.

1 .- 20 . (canceled) 
     
     
         21 . A system comprising:
 (a) a plurality of compartments, wherein each compartment of a subset of the plurality of compartments comprises:
 (i) a cell; and 
 (ii) a scaffold comprising:
 (A) an effector bound to the scaffold via a cleavable linker, wherein the effector is releasable from the scaffold via cleavage of the cleavable linker to generate a released effector into the compartment; and 
 (B) a first barcode corresponding to and for identifying the effector; and 
 
   (b) at least one of:
 (i) a sorting device for sorting at least one of: a compartment, contents of a compartment, a scaffold of a compartment, a first barcode of a compartment, or a cell of a compartment, of the subset of the plurality of compartments, based on a property of a signal indicative of an effect of the released effector on the cell; 
 (ii) a tagging reagent present in the subset of the plurality of compartments comprising a second barcode for tagging the scaffold or the effector based on a property of a signal indicative of an effect of the released effector on the cell; or 
 (iii) an injection module for adding an injected reagent into a compartment of the subset of the plurality of compartments based on a property of a signal indicative of an effect of the released effector on the cell. 
   
     
     
         22 . The system of  claim 21 , wherein the compartment is a droplet, a well, a micro-well, a microfluidic confinement, or a combination thereof. 
     
     
         23 . The system of  claim 21 , wherein the scaffold is a particle with a diameter of at least about 1 micrometer (μm). 
     
     
         24 . The system of  claim 21 , wherein the effector comprises a subunit of the effector, and the first barcode comprises a subunit of the first barcode corresponding to and for identifying the effector or the subunit of the effector. 
     
     
         25 . The system of  claim 21 , wherein the cleavable linker is a photocleavable linker configured to release the effector upon exposure to light. 
     
     
         26 . The system of  claim 25 , further comprising a light source for exposing the cleavable linker to light to release the effector from the scaffold. 
     
     
         27 . The system of  claim 21 , wherein the first barcode is a nucleic acid molecule, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), a peptide, or a peptide nucleic acid (PNA). 
     
     
         28 . The system of  claim 21 , wherein the subset of the plurality of compartments further comprises an assay reagent for assessing an effect of the released effector on the cell and producing a signal indicative of the effect. 
     
     
         29 . The system of  claim 28 , wherein the assay reagent comprises a probe for generating the signal upon interacting with the cell. 
     
     
         30 . The system of  claim 21 , wherein the sorting device performs the sorting via generating a stimulus for stimulating or initiating a movement of the compartment, the contents of the compartment, the scaffold, the barcode, the cell, or any combination thereof, based on the signal. 
     
     
         31 . The system of  claim 30 , wherein the stimulus comprises a pulse, a voltage differential or charge gradient, an electrical field gradient, a sound, a pressure differential or gradient, a radiation pressure, an optical stimulus, a light beam or laser, electro-osmosis, electrophoresis, dielectrophoresis, mechanical switching, gravity, a change in the geometry of a microfluidic channel or channel squeezing, fluid flow, or any combination thereof. 
     
     
         32 . The system of  claim 21 , wherein the system further comprises a waveform pulse generator, an electrode, an electrical field generator, an optical tweezer, a light source or laser, a diaphragm, a pressure source, a flow reservoir, tubing and tubing connection, a valve, a pump, a pressure controller, electro-osmotic flow control, an electrophoresis module, a dielectrophoresis module, a collection chamber or container, a cell trapper, an injection module, a computer, an algorithm, or any combination thereof. 
     
     
         33 . The system of  claim 21 , further comprising a detector for detecting the signal. 
     
     
         34 . The system of  claim 33 , wherein the detector comprises a computer, an optical detector, a microscope, a camera, an image processing device, a light source, a laser, a photon counter, a computer, a microprocessor, an algorithm, a computer program, or any combination thereof. 
     
     
         35 . The system of  claim 21 , wherein the injection module comprises a pico-injection module or a droplet merging module. 
     
     
         36 . The system of  claim 21 , wherein the tagging comprises attaching the first barcode to the second barcode. 
     
     
         37 . The system of  claim 36 , wherein the first barcode and the second barcode are nucleic acid molecules, and wherein the attaching comprises ligating the second barcode to the first barcode, annealing the second barcode to the first barcode, hybridizing the second barcode to the first barcode, amplifying the second barcode onto the first barcode, extending the first barcode, or any combination thereof. 
     
     
         38 . The system of  claim 21 , wherein the first barcode comprises a first sequence, the second barcode comprises a second sequence, and the first sequence is complementary to the second sequence. 
     
     
         39 . The system of  claim 21 , wherein the first barcode further identifies the scaffold. 
     
     
         40 . The system of  claim 39 , wherein the first barcode is a nucleic acid barcode comprising an effector-specific sequence for identifying the effector, and a scaffold-specific sequence for identifying the scaffold. 
     
     
         41 . The system of  claim 21 , wherein the injected reagent comprises a cleaving reagent for cleaving the first barcode or the effector, a lysis buffer for lysing the cell, an assay reagent, the second barcode, or any combination thereof.