WHAT IS CLAIMED IS:
`
`1.
`
`A method comprising: a. subdividing a plurality of adaptors into a
`
`plurality of first partitions, wherein each of said first partitions has on average a first volume and
`
`wherein said adaptors comprise unique barcodes, b. subdividing a sample comprising multiple
`
`polynucleotides into a plurality of second partitions, wherein each of said second partitions has
`
`on average a second volume, wherein said second volume is greater than said f1rstvolume, c.
`
`merging at least one of said first partitions with at least one of said second partitions to form a
`
`merged partition, and d. tagging one of said multiple polynucleotides, or fragment thereof, with
`
`at least one of said adaptors.
`
`2. A method comprising: a. subdividing a plurality of adaptors into a plurality of first partitions,
`
`wherein each of said first partitions has on average a first volume and wherein said adaptors
`
`comprise unique barcodes, b. subdividing a sample comprising multiple polynucleotides into a
`
`plurality of second partitions, wherein each of said second partitions has on average a second
`
`volume, wherein said second volume is less than said f1rstvolume, c. merging at least one of said
`
`first partitions with at least one of said second partitions to form a merged partition, and d.
`
`tagging one of said multiple polynucleotides, or fragment thereof, with at least one of said
`
`adaptors.
`
`3. The method of claim 1 or 2, wherein said first partitions are droplets.
`
`4. The method of claim 3, wherein said second partitions are droplets.
`
`5. The method of claim 3, wherein said droplets are within an immiscible fluid.
`
`6. The method of claim 1 or 2, wherein said polynucleotides are genomic DNA.
`
`7. The method of claim 4, wherein said tagging comprises merging at least one first droplet
`
`comprising one of said adaptors with at least one second droplet comprising one of said
`
`polynucleotides.
`
`8. The method of claim 1, wherein said first partitions are first droplets and said second partitions
`
`68
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`

`

`are second droplets; and wherein, prior to said merging, said at least one second droplet
`
`comprises said at least one first droplet.
`
`9. The method of claim 1, wherein said first partitions are first droplets and said second partitions
`
`are second droplets; and wherein, prior to said merging, said at least one second droplet does not
`
`comprise said at least one first droplet.
`
`10. The method of claim 2, wherein said first partitions are first droplets and said second
`
`partitions are second droplets, and wherein, prior to said merging, said at least one first droplet
`
`comprises said at least one second droplet.
`
`11. The method of claim 2, wherein said first partitions are first droplets and said second
`
`partitions are second droplets, and wherein, prior to said merging, said at least one first droplet
`
`does not comprise said at least one second droplet.
`
`12. The method of claim 1, wherein said second volume is at least two times said volume of said
`
`first volume.
`
`13. The method of claim 2, wherein said first volume is at least two times said volume of said
`
`second volume.
`
`14. The method of claim 7, further comprising modifying the temperature of said droplets.
`
`15. The method of claim 7, wherein said merging comprises use of a controller such that each of
`
`said first droplets merges with each of said second droplets.
`
`16. The method of claim 7, wherein said merging comprises randomly merging droplets
`
`comprising polynucleotides with droplets comprising adaptors.
`
`17. The method of claim 1, further comprising pooling said adaptor-tagged polynucleotides, or
`
`fragments thereof.
`
`18. The method of claim 1, further comprising analyzing said adaptor-tagged polynucleotides, or
`
`69
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`

`

`fragments thereof.
`
`19. The method of claim 18, wherein said analyzing comprises sequencing said adaptor-tagged
`
`polynucleotides, or fragments thereof.
`
`20. The method of claim 1, further comprising determining whether said adaptor-tagged
`
`polynucleotides, or fragments thereof, were located in the same partition.
`
`21. The method of claim 19, further comprising estimating the likelihood that any two sequence
`
`reads generated by said sequencing came from the same or different partitions.
`
`22. The method of claim 6, wherein said sample is partitioned so that it is unlikely that a given
`
`partition comprises two or more polynucleotides, or fragments thereof, from the same locus but
`
`from different chromosomes.
`
`23. The method of claim 6, wherein said genomic DNA is high molecular-weight DNA.
`
`24. The method of claim 1 or 2, further comprising fragmenting said polynucleotides within said
`
`second partitions to form polynucleotide fragments.
`
`25. The method of claim 24, wherein said polynucleotides fragments are generated by
`
`fragmenting said polynucleotides with an endonuclease.
`
`26. The method of claim 1, wherein said polynucleotides are tagged by ligating said adaptors to
`
`said polynucleotides within a plurality of said merged partitions.
`
`27. The method of claim 1, wherein said tagging is accomplished using transposons.
`
`28. The method of claim 1, wherein said tagged polynucleotides are amplified.
`
`29. The method of claim 28, wherein said amplif1cation comprises a polymerase chain reaction.
`
`30. The method of claim 1, wherein said polynucleotides are amplified before tagging.
`
`7O
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`

`

`31. The method of claim 1 or 2, wherein each of said first partitions comprises, on average, less
`
`than five adaptors.
`
`32. The method of claim 1 or 2, wherein each of said second partitions comprises, on average,
`
`less than five of said multiple polynucleotides.
`
`33. The method of claim 1, wherein said subdividing of said sample comprises emulsifying or
`
`mixing said sample with said second partitions.
`
`34. The method of claim 2, wherein said subdividing of said plurality of adaptors comprises
`
`emulsifying or mixing said plurality of adaptors with said second partitions.
`
`35. The method of claim 30, wherein said amplification is multiple-displacement amplification.
`
`36. A method comprising a. partitioning organelles into a plurality of partitions, wherein each
`
`partition comprises on average less than five organelles per partition, b. lysing said extracellular
`
`organelles in the plurality of partitions, wherein the lysing releases RNA from said organelles, c.
`
`generating tagged cDNA from said released RNA in said plurality of partitions with adaptors
`
`comprising a barcode, wherein each partition in the plurality of partitions comprises adaptors
`
`with a unique barcode.
`
`37. The method of claim 36, wherein said organelles are extracellular organelles.
`
`38. The method of claim 36, wherein said organelles are exosomes.
`
`39. The method of claim 36, wherein said generating tagged cDNA comprises reverse
`
`transcription of said released RNA with partition-specific barcoded primers.
`
`40. The method of claim 36, further comprising sequencing said tagged cDNA.
`
`41. The method of claim 36, further comprising determining if said tagged cDNA is from the
`
`same organelle.
`
`7l
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`

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`42. A method comprising a. partitioning microorganisms into a plurality of partitions, b.
`
`obtaining polynucleotides from the microorganisms in the plurality of partitions; and c. tagging
`
`the polynucleotides in the plurality of partitions with adaptors comprising a barcode, wherein
`
`each partition in the plurality of partitions comprises adaptors with a unique barcode.
`
`43. The method of claim 42, wherein each of said partitions comprises, on average, less than five
`
`microorganisms.
`
`44. The method of claim 42, further comprising sequencing the tagged polynucleotides.
`
`45. The method of claim 42, further comprising determining if the tagged polynucleotide
`
`fragments are from the same partition.
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`72
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`

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