Compositions and methods for sample processing
First Claim
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1. A method of processing a template nucleic acid sequence, comprising:
- (a) co-partitioning a template nucleic acid sequence and a bead comprising a plurality of oligonucleotides releasably attached thereto into a partition, wherein each oligonucleotide of the plurality of oligonucleotides comprises a sequence comprising a common barcode sequence and a primer sequence complementary to one or more regions of the template nucleic acid sequence;
(b) annealing the primer sequence of an oligonucleotide of the plurality of oligonucleotides to the template nucleic acid sequence; and
(c) extending the primer sequence to produce an extension product complementary to at least a portion of the template nucleic acid sequence, the extension product comprising the primer sequence and the common barcode sequence,wherein, after (a), the sequence of the oligonucleotide is released from the bead into the partition, andwherein, after (c), the extension product is in solution within the partition.
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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
75 Claims
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1. A method of processing a template nucleic acid sequence, comprising:
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(a) co-partitioning a template nucleic acid sequence and a bead comprising a plurality of oligonucleotides releasably attached thereto into a partition, wherein each oligonucleotide of the plurality of oligonucleotides comprises a sequence comprising a common barcode sequence and a primer sequence complementary to one or more regions of the template nucleic acid sequence; (b) annealing the primer sequence of an oligonucleotide of the plurality of oligonucleotides to the template nucleic acid sequence; and (c) extending the primer sequence to produce an extension product complementary to at least a portion of the template nucleic acid sequence, the extension product comprising the primer sequence and the common barcode sequence, wherein, after (a), the sequence of the oligonucleotide is released from the bead into the partition, and wherein, after (c), the extension product is in solution within the partition. - 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40)
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41. A method of processing a template nucleic acid sequence, comprising:
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(a) co-partitioning a template nucleic acid sequence and a bead comprising a plurality of oligonucleotides releasably attached thereto into a partition, wherein each oligonucleotide of the plurality of oligonucleotides comprises a sequence comprising a common barcode sequence and a primer sequence complementary to one or more regions of the template nucleic acid sequence, wherein the plurality of oligonucleotides comprises (i) a first oligonucleotide comprising a first sequence comprising the common barcode sequence and a first primer sequence and (ii) a second oligonucleotide comprising a second sequence comprising the common barcode sequence and a variable primer sequence; (b) annealing the first primer sequence of the first oligonucleotide to the template nucleic acid sequence; (c) extending the first primer sequence to produce a first extension product complementary to at least a portion of the template nucleic acid sequence, the first extension product comprising the first primer sequence and the common barcode sequence; (d) annealing the variable primer sequence of the second oligonucleotide to the first extension product; and (e) extending the variable primer sequence to produce a second extension product complementary to at least a portion of the first extension product, the second extension product comprising the variable primer sequence and the common barcode sequence, wherein, after (a), the first sequence of the first oligonucleotide is released from the bead into the partition, and wherein, after (c), the first extension product is in solution within the partition. - View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75)
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Specification