Manipulating and detecting biological samples

Abstract

Disclosed herein, inter alia, are compositions and methods for efficient transfer and analyses of cellular material, tissue samples, such as tissue sections, using carrier substrates.

1 . A method of detecting a biomolecule in a tissue section, said method comprising:
 a) contacting the tissue section with a carrier substrate, thereby immobilizing the tissue section onto said carrier substrate and generating a sample-carrier construct, wherein said carrier substrate comprises a first adhesion strength;   b) contacting the tissue section of the sample-carrier construct with a receiving substrate to generate an immobilized tissue section, wherein said receiving substrate comprises a second adhesion strength, wherein the second adhesion strength is greater than the first adhesion strength;   c) removing the carrier substrate from the immobilized tissue section;   d) permeabilizing the immobilized tissue section; and   e) contacting said biomolecule in said tissue section with a detection agent, thereby detecting the biomolecule in the tissue section, wherein the detection agent comprises a fluorophore.   
     
     
         2 . The method of  claim 1 , wherein step c) occurs prior to step e). 
     
     
         3 . The method of  claim 1 , wherein step c) occurs prior to step d). 
     
     
         4 . The method of  claim 1 , wherein generating a sample-carrier construct comprises forming a plurality of non-covalent bonds between the tissue section and the carrier substrate. 
     
     
         5 . The method of  claim 1 , wherein the carrier substrate comprises water molecules attached to the surface of said carrier substrate. 
     
     
         6 . The method of  claim 1 , wherein the carrier substrate comprises a compression modulus greater than about 100 kPa. 
     
     
         7 . The method of  claim 1 , wherein generating an immobilized tissue section comprises forming a plurality of covalent bonds between the tissue section and the receiving substrate. 
     
     
         8 . The method of  claim 1 , wherein the receiving substrate comprises (3-aminopropyl)triethoxysilane (APTES), (3-Aminopropyl)trimethoxysilane (APTMS), γ-Aminopropylsilatrane (APS), N-(6-aminohexyl)aminomethyltriethoxysilane (AHAMTES), polyethylenimine (PEI), 5,6-epoxyhexyltriethoxysilane, or triethoxysilylbutyraldehyde, or a combination thereof. 
     
     
         9 . The method of  claim 1 , wherein the biomolecule is a nucleic acid sequence, carbohydrate, or protein. 
     
     
         10 . The method of  claim 1 , wherein the biomolecule is a nucleic acid sequence. 
     
     
         11 . The method of  claim 10 , further comprising amplifying the nucleic acid sequence to generate amplification products. 
     
     
         12 . The method of  claim 11 , further comprising detecting the amplification products. 
     
     
         13 . The method of  claim 1 , wherein the detection agent comprises a protein-specific binding agent. 
     
     
         14 .- 15 . (canceled) 
     
     
         16 . The method of  claim 1 , further comprising digesting the tissue section by contacting the sample-carrier construct with an endopeptidase. 
     
     
         17 . The method of  claim 10 , wherein step e) comprises hybridizing a sequencing primer to the biomolecule and sequencing the biomolecule. 
     
     
         18 .- 24 . (canceled) 
     
     
         25 . The method of  claim 1 , wherein the thickness of the tissue section is about 1 μm to about 20 μm. 
     
     
         26 . The method of  claim 1 , wherein the carrier substrate comprises agarose, amylose, amylopectin, alginate, gelatin, cellulose, polyolefin, polyethylene glycol, polyvinyl alcohol, and/or acrylate polymers and copolymers thereof. 
     
     
         27 . The method of  claim 1 , wherein the carrier substrate comprises agarose, amylose, or amylopectin. 
     
     
         28 . (canceled) 
     
     
         29 . The method of  claim 1 , wherein the carrier substrate further comprises a support scaffold, wherein said support scaffold is a thermoplastic elastomer. 
     
     
         30 . The method of  claim 1 , wherein the carrier substrate comprises a Young's modulus of about 5 kPa to about 30 kPa. 
     
     
         31 . (canceled) 
     
     
         32 . The method of  claim 1 , wherein the carrier substrate comprises about 80% to about 99% water. 
     
     
         33 . The method of  claim 1 , wherein the receiving substrate comprises a functionalized glass surface or a functionalized plastic surface. 
     
     
         34 . The method of  claim 1 , wherein prior to contacting the tissue section with the receiving substrate, the sample-carrier construct is stored for one or more days. 
     
     
         35 .- 36 . (canceled) 
     
     
         37 . The method of  claim 34 , wherein the sample-carrier construct is stored at less than about 25° C. 
     
     
         38 .- 39 . (canceled) 
     
     
         40 . The method of  claim 1 , wherein removing the carrier substrate comprises physically removing, thermally removing, chemically removing, or enzymatically removing. 
     
     
         41 .- 98 . (canceled) 
     
     
         99 . The method of  claim 1 , wherein the sample-carrier construct comprises substantially uniform adhesion between the tissue section and the carrier substrate. 
     
     
         100 . The method of  claim 1 , wherein the carrier substrate comprises a polymerized hydrogel. 
     
     
         101 . The method of  claim 1 , wherein substantially all of the tissue section is immobilized to the receiving substrate. 
     
     
         102 . The method of  claim 1 , wherein prior to step a), the carrier substrate is solid or semi-solid. 
     
     
         103 . The method of  claim 40 , wherein physically removing said carrier substrate comprises mechanically pulling or lifting thereby detaching said carrier substrate.