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 - 20 . (canceled)
21 . A method for analyte detection, the method comprising the steps of:
exposing a plurality of binding agents comprising oligonucleotides to a plurality of target molecules of a sample,
thereby binding one or more of the plurality of binding agents to target molecules of the plurality of target molecules and forming one or more complexes comprising a target molecule linked via one of the binding agents to a nucleic acid sequence that includes a barcode sequence; and
identifying a target molecule in a given complex of the one or more complexes by detecting the barcode sequence in the given complex.
22 . The method of claim 21 , further comprising conducting a nucleic acid amplification reaction with one or more of the complexes.
23 . The method of claim 22 , wherein the amplification reaction comprises a rolling circle amplification reaction.
24 . The method of claim 21 , wherein the sample is a tissue sample.
25 . The method of claim 24 , wherein the tissue sample comprises cells from a tissue biopsy.
26 . The method of claim 24 , wherein the tissue sample comprises a plurality of different target molecules.
27 . The method of claim 26 , wherein target molecules of the plurality of target molecules are associated with a unique nucleic acid sequence of a binding agent.
28 . The method of claim 21 , wherein the binding agents comprise oligonucleotide probes.
29 . The method of claim 28 , wherein the oligonucleotide probes comprise padlock probes.
30 . The method of claim 29 , wherein the padlock probes hybridize to their targets and ligase produces a circular DNA.
31 . The method of claim 21 , wherein the identifying step comprises fluorescence detection.
32 . The method of claim 31 , wherein the fluorescence detection detects fluorescence specific to the barcode sequence.
33 . The method of claim 21 , wherein the identifying step comprises sequencing the barcode sequence in the given complex.