Methods and compositions for labeling targets

A method of labeling a target in a sample for quantification of said target, comprising:

• hybridizing said target with a first oligonucleotide comprising a first universal adaptor sequence and a target-specific sequence;
• extending said first oligonucleotide to generate a first nucleotide sequence;
• hybridizing said first nucleotide sequence with a second oligonucleotide comprising a second universal adaptor sequence and a second target-specific sequence;
• extending said second oligonucleotide to generate a second nucleotide sequence;
• hybridizing said second nucleotide sequence with a third oligonucleotide comprising a binding site for a first amplification primer and the first universal adaptor sequence;
• extending said third oligonucleotide to generate a third nucleotide sequence;
• hybridizing said third nucleotide sequence with a fourth oligonucleotide comprising a binding site for a second amplification primer and the second universal adaptor sequence, wherein one or both of the third oligonucleotide and the fourth oligonucleotide comprises part of a stochastic barcode;
• extending said fourth oligonucleotide to generate a fourth nucleotide sequence;
• and
• amplifying said fourth nucleotide sequence using a first amplification primer and a second amplification primer to generate a plurality of a fifth nucleotide sequences,
• wherein each of the plurality of the fifth nucleotide sequences comprises said target and the stochastic barcode.

A method of labeling a target in a sample for quantification of said target, comprising:

• hybridizing said target with a first oligonucleotide comprising a target-specific sequence and a binding site for a first amplification primer;
• extending said first oligonucleotide to generate a first nucleotide sequence;
• hybridizing said first nucleotide sequence with a second oligonucleotide comprising a universal adaptor sequence and a second target-specific sequence;
• extending said second oligonucleotide to generate a second nucleotide sequence;
• hybridizing said second nucleotide sequence with a third oligonucleotide comprising a binding site for a second amplification primer and a sequence that specifically binds the universal adaptor sequence, wherein one or both of the second oligonucleotide and the third oligonucleotide comprises part of a stochastic barcode;
• extending said third oligonucleotide to generate a third nucleotide sequence;
• and
• amplifying said third nucleotide sequence using a first amplification primer and a second amplification primer to generate a plurality of a fourth nucleotide sequences,
• wherein each of the plurality of the fourth nucleotide sequences comprises said target and the stochastic barcode.

A method of characterizing a sample, comprising:

• hybridizing a first target in the sample with a first oligonucleotide comprising a first target-specific sequence and a first stochastic barcode, wherein the first target is an mRNA encoding a TCR alpha chain or beta chain;
• hybridizing a second target in the sample with a second oligonucleotide comprising a second target-specific sequence and a second stochastic barcode;
• extending the first oligonucleotide and the second oligonucleotide to incorporate the first stochastic barcode into the first target and the second stochastic barcode into the second target;
• and
• identifying the sequences of the first target and the second target.