COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
First Claim
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1. A method of characterizing a nucleic acid segment, comprising:
- co-partitioning the nucleic acid segment and a bead comprising a plurality of oligonucleotides that comprise a common nucleic acid barcode sequence into a partition;
attaching the oligonucleotides to fragments of the nucleic acid segment or to copies of portions of the nucleic acid segment, thereby attaching the common nucleic acid barcode sequence to the fragments of the nucleic acid segment or to the copies of the portions of the nucleic acid segment;
sequencing the fragments of the nucleic acid segment or the copies of the portions of the nucleic acid segment and the attached common nucleic acid barcode sequence; and
characterizing the fragments or the copies of the portions of the nucleic acid segment as being linked within the nucleic acid segment based at least in part, upon their attachment to the common nucleic acid barcode sequence.
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Abstract
This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
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Citations
37 Claims
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1. A method of characterizing a nucleic acid segment, comprising:
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co-partitioning the nucleic acid segment and a bead comprising a plurality of oligonucleotides that comprise a common nucleic acid barcode sequence into a partition; attaching the oligonucleotides to fragments of the nucleic acid segment or to copies of portions of the nucleic acid segment, thereby attaching the common nucleic acid barcode sequence to the fragments of the nucleic acid segment or to the copies of the portions of the nucleic acid segment; sequencing the fragments of the nucleic acid segment or the copies of the portions of the nucleic acid segment and the attached common nucleic acid barcode sequence; and characterizing the fragments or the copies of the portions of the nucleic acid segment as being linked within the nucleic acid segment based at least in part, upon their attachment to the common nucleic acid barcode sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
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31. A method of characterizing a target nucleic acid, comprising:
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partitioning first fragments of the target nucleic acid into a plurality of droplets, each droplet of the plurality of droplets comprising a bead having a plurality of oligonucleotides attached thereto, the oligonucleotides attached to a given bead comprising a common barcode sequence; attaching the common barcode sequence to second fragments of the first fragments; pooling the plurality of droplets; sequencing the second fragments and attached barcode sequences; and mapping a plurality of the second fragments to one or more of the first fragments based, at least in part, upon the plurality of second fragments comprising a common barcode sequence.
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32. A method of sequencing nucleic acids, comprising:
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providing a plurality of target nucleic acid sequences; separating the target nucleic acid sequences into a plurality of separate partitions, each partition of the plurality of separate partitions comprising one or more target nucleic acid sequences, and a bead having a plurality of oligonucleotides attached thereto, the oligonucleotides attached to a given bead comprising a common barcode sequence; attaching the oligonucleotides to fragments of the one or more target nucleic acid sequences or to copies of portions of the one or more target nucleic acid sequences within a partition, thereby attaching the common barcode sequence to the fragments of the one or more target nucleic acid sequences or to the copies of the portions of the one or more target nucleic acid sequences; pooling the plurality of separate partitions; and sequencing the fragments of the one or more target nucleic acid sequences or the copies of the portions of the one or more target nucleic acid sequences and attached barcode sequences to provide barcoded fragment sequences or barcoded copy sequences. - View Dependent Claims (33)
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34. A method of characterizing a nucleic acid segment, comprising:
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co-partitioning the nucleic acid segment, and a bead comprising a plurality of oligonucleotides that comprise a common nucleic acid barcode sequence, into a first droplet; attaching the oligonucleotides to fragments of the nucleic acid segment or to copies of portions of the nucleic acid segment, thereby attaching the common nucleic acid barcode sequence to the fragments of the nucleic acid segment or to the copies of the portions of the nucleic acid segment; sequencing the fragments of the nucleic acid segment or the copies of the portions of the nucleic acid segment and attached common nucleic acid barcode sequence to provide a plurality of barcoded fragment sequences or a plurality of barcoded copy sequences; and assembling the plurality of the barcoded fragment sequences or the plurality barcoded copy sequences into one or more contiguous nucleic acid sequences based at least in part on the common nucleic acid barcode sequence. - View Dependent Claims (35)
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36. A method of sequencing nucleic acids, comprising:
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providing a plurality of target nucleic acid sequences; separating the target nucleic acid sequences into a plurality of separate partitions, each partition of the plurality of separate partitions comprising one or more target nucleic acid sequences, and a plurality of oligonucleotides, the oligonucleotides in a given partition comprising a common barcode sequence, and wherein the plurality of separate partitions comprise at least 10,000 different barcode sequences; attaching the common barcode sequence in each partition to fragments of the one or more target nucleic acid sequences or to copies of portions of the one or more target nucleic acid sequences within the partition; pooling the plurality of separate partitions; and sequencing the fragments of the one or more target nucleic acid sequences or the copies of the portions of the one or more target nucleic acid sequences and attached barcode sequences. - View Dependent Claims (37)
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Specification