Methods and compositions for whole transcriptome amplification

1. A method for labeling a plurality of nucleic acid targets from a sample, comprising:

hybridizing the plurality of nucleic acid targets from the sample with a plurality of labeling nucleic acids each comprising a first universal label;

extending the plurality of labeling nucleic acids to generate a plurality of first strand polynucleotides, wherein the plurality of nucleic acid targets are single-stranded;

synthesizing a plurality of second strand polynucleotides using the plurality of first strand polynucleotides as templates to generate a plurality of double-stranded polynucleotides;

ligating an adaptor to the plurality of double-stranded polynucleotides, wherein said adaptor comprises a second universal label; and

amplifying the plurality of double-stranded polynucleotides using the first universal label and the second universal label as primer sequences, thereby generating a plurality of amplicons comprising the plurality of nucleic acid targets.

2. The method of claim 1 , wherein each of the plurality of labeling nucleic acids comprises a stochastic barcode.

3. The method of claim 2 , wherein said stochastic barcode comprises a molecular label, a cellular label, a target-specific region, or any combination thereof.

4. The method of claim 1 , wherein the plurality of nucleic acid targets are mRNAs.

5. The method of claim 4 , wherein synthesizing the plurality of second strand polynucleotides comprises nicking the plurality of mRNAs with an RNase, thereby generating one or more mRNA primers.

6. The method of claim 4 , wherein the plurality of nucleic acid targets are nucleic acids from a single cell selected from the group consisting of a bacterial cell, a fungal cell, a protozoan cell, an animal cell, and a plant cell.

7. The method of claim 4 , wherein the plurality of amplicons comprises a whole transcriptome amplification (WTA) product.

8. The method of claim 1 , wherein each of the plurality of labeling nucleic acids is immobilized on a solid support.

9. The method of claim 8 , wherein said solid support is a bead.

10. The method of claim 8 , wherein at least two of said plurality of labeling nucleic acids immobilized on a single solid support comprises different molecular labels.

11. The method of claim 8 , wherein said plurality of labeling nucleic acids attached to a solid support comprises the same cellular label.

12. The method of claim 1 , wherein the sample comprises a single cell.

13. The method of claim 1 , wherein the first universal label and the second universal label are different.

14. A method for labeling a plurality of nucleic acid targets from a sample comprising:

hybridizing the plurality of nucleic acid targets from the sample with a plurality of labeling nucleic acids each comprising a first universal label;

extending the plurality of labeling nucleic acids to generate a plurality of first strand polynucleotides, wherein the plurality of first stand polynucleotides and the plurality of nucleic acid targets form a plurality of double-stranded polynucleotides;

contacting the plurality of double-stranded polynucleotides with a first transposome comprising a first transposase and a first adaptor, wherein said first adaptor comprises a second universal label;

ligating the first adaptor to the double-stranded polynucleotides with the first transposase to generate a plurality of double stranded polynucleotides that are ligated with the first adaptor; and

amplifying the plurality of double-stranded polynucleotides that are ligated with the first adaptor using the first universal label and the second universal label as primer sequences, thereby generating a plurality of amplicons comprising the plurality of nucleic acid targets.

15. The method of claim 14 , further comprising synthesizing a plurality of second strand polynucleotides using the plurality of first strand polynucleotides as templates.

16. The method of claim 14 , wherein said first adaptor comprises a stochastic barcode.

17. The method of claim 14 , wherein said second universal label is a transposome sequence.

18. The method of claim 14 , wherein each of the plurality of labeling nucleic acids is immobilized on a solid support.

19. The method of claim 18 , wherein said solid support is a bead.

20. The method of claim 19 , comprising purifying double-stranded polynucleotides that are immobilized on beads, wherein the double-stranded polynucleotides are double-stranded polynucleotides that are ligated with the first adaptor, the second adaptor, or both.

21. A method for labeling a plurality of nucleic acid target sequences from a single cell, comprising:

providing the single cell to a partition comprising a solid support immobilized with a plurality of labeling nucleic acids each comprising a first universal label, wherein the single cell is a bacterial cell, a fungal cell, a protozoan cell, an animal cell, or a plant cell;

lysing the single cell to release the plurality of nucleic acid target sequences, wherein the nucleic acid target sequences are mRNAs;

hybridizing the plurality of nucleic acid target sequences from the single cell with the plurality of labeling nucleic acids;

extending the plurality of labeling nucleic acids to generate a plurality of first strand polynucleotides;

adding an adaptor sequence to the plurality of first strand polynucleotides, wherein said adaptor sequence comprises a second universal label; and

amplifying the plurality of first strand polynucleotides using the first universal label and the second universal label as primer sequences, thereby generating a plurality of amplicons comprising the plurality of nucleic acid target sequences.

22. The method of claim 21 , wherein said adaptor sequence is added by a transposome.

23. The method of claim 21 , wherein said adaptor is added by a ligation step.