Compositions and methods for molecular labeling
The invention provides barcode libraries and methods of making and using them including obtaining a plurality of nucleic acid constructs in which each construct comprises a unique N-mer and a functional N-mer and segregating the constructs into a fluid compartments such that each compartment contains one or more copies of a unique construct. The invention further provides methods for digital PCR and for use of barcode libraries in digital PCR.
1. A method for protein detection, the method comprising:
introducing a protein-specific binding reagent linked to an oligonucleotide barcode to a sample comprising a population of cells;
encapsulating the cells in sample droplets such that each sample droplet comprises a single cell and said protein-specific binding reagent by merging droplets containing said cells and said protein-specific binding reagents; and
determining the presence of proteins of said cells that are bound to said protein-specific binding reagents.
2. The method of claim 1 , further comprising the step of lysing said cells.
3. The method of claim 1 , wherein said protein-specific binding reagent is selected from an antibody, an aptamer, a nucleic acid-labeled protein.
4. The method of claim 1 , wherein the protein-specific binding reagents are coupled to beads.
5. The method of claim 1 , wherein the protein-specific binding reagents are cleavable from the proteins to which they bind.
6. The method of claim 1 , wherein the proteins are cell-surface proteins.
7. The method of claim 1 , wherein the encapsulating step comprises loading the cells into a microfluidic chip.
8. The method of claim 1 , wherein the protein-specific binding reagents further comprise a universal binding site.
9. The method of claim 1 , further comprising quantifying the proteins.
10. The method of claim 1 , wherein the oligonucleotide barcodes linked to the protein-specific binding reagents have ligation-competent ends and the method includes ligating copies of droplet-identifying barcodes to the oligonucleotide barcodes linked to said protein-specific binding reagents.
11. The method of claim 2 , wherein lysing occurs within said droplets.