System and methods for massively parallel analysis of nucleic acids in single cells

1. A method for creating a library of polynucleotides, comprising the steps of:

introducing multiple sets of initial probes into a plurality of compartments under conditions selected such that more than a half of the plurality of compartments contain one or less than one set of the initial probes, wherein each set of the initial probes comprises (1) an initial forward probe, wherein the initial forward probe (i) is affixed to a bead or a solid surface, and (ii) comprises a sequence complementary to a first subsequence of a first target sequence and one of at least 1,000 unique barcode sequences, and (2) an initial reverse probe, wherein the initial reverse probe comprises (i) a sequence complementary to a second subsequence of the first target sequence and (ii) a sequence complementary to a non-human, exogenous sequence;

introducing multiple sets of second probes into the plurality of compartments, wherein each set of the second probes comprises (1) a second forward probe, wherein the second forward probe comprises (i) the non-human, exogenous sequence and (ii) a sequence that is complementary to a first subsequence of a second target sequence, and (2) a second reverse probe comprising a sequence that is complementary to a second subsequence to the second target sequence;

amplifying the first target sequence using the multiple sets of the initial probes;

amplifying the second target sequence using the multiple sets of the second probes;

hybridizing the non-human exogenous sequence to its complement; and

amplifying a fused sequence comprising one of the at least 1,000 barcode sequences, the first target sequence and the second target sequence, thereby generating a library of fused polynucleotides, wherein each of the fused polynucleotides comprises one of the at least 1,000 unique barcode sequences.

2. The method of claim 1 , further comprising the step of:

bulk sequencing the library of fused polynucleotides.

3. The method of claim 2 , further comprising the step of:

separating a plurality of single cells from a population of at least 10,000 cells into the plurality of compartments.

4. The method of claim 3 , further comprising the step of:

identifying at least one of the plurality of compartments based on the unique barcode sequences.

5. The method of claim 3 , further comprises the step of:

identifying a sequence that comprises one of the unique barcode sequences; and

tracing a cell that the sequence originates from.

6. The method of claim 3 , wherein the plurality of compartments comprises emulsion microdroplets.

7. The method of claim 1 , wherein the first target sequence and the second target sequence are RNA molecules.

8. The method of claim 7 , wherein the steps of amplifying the first target sequence and the second target sequence comprise: performing RT-PCR.

9. The method of claim 1 , wherein the first target sequence and the second target sequence are DNA molecules.

10. The method of claim 9 , wherein the steps of amplifying the first target sequence and the second target sequence comprise: performing a polymerase chain reaction.

11. The method of claim 9 , wherein the steps of amplifying the first target sequence and the second target sequence comprise: a ligase chain reaction.

12. The method of claim 3 , wherein the single cell is contained in a population of at least 25,000 cells.

13. The method of claim 12 , wherein the single cell is contained in a population of at least 50,000 cells.

14. The method of claim 13 , wherein the single cell is contained in a population of at least 75,000 cells.

15. The method of claim 14 , wherein the single cell is contained in a population of at least 100,000 cells.

16. The method of claim 1 , wherein the first target sequence and the second target sequence are human sequences.