METHODS AND COMPOSITIONS FOR LABELING CELLS
First Claim
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1. A method for analyzing cellular occupancy of partitions, comprising:
- (a) contacting a plurality of cells with a plurality of labelling molecules comprising a plurality of cell nucleic acid barcode sequences to generate a plurality of labelled cells, wherein each of said plurality of labelled cells comprises a different cell nucleic acid barcode sequence;
(b) generating a plurality of partitions comprising said plurality of labelled cells and a plurality of beads, wherein said plurality of beads comprise a plurality of partition nucleic acid barcode sequences coupled thereto, wherein each of said plurality of partitions comprises a different partition nucleic barcode sequence, and wherein at least a fraction of said plurality of partitions comprises more than one labelled cell of said plurality of labelled cells;
(c) within said plurality of partitions, (i) using partition nucleic acid barcode sequences of said plurality of partition nucleic acid barcode sequences and cell nucleic acid barcode sequences of said plurality of cell nucleic acid barcode sequences to synthesize a plurality of barcoded nucleic acid products, and (ii) releasing or recovering said plurality of barcoded nucleic acid products or derivatives thereof from said plurality of partitions; and
(d) identifying-sequencing said plurality of barcoded nucleic acid products or derivatives thereof to determine that at least two labelled cells of said plurality of labelled cells originate from a same partition using (i) said cell nucleic acid barcode sequences of said plurality of cell nucleic acid barcode sequences or complements thereof and (ii) said partition nucleic acid barcode sequences of said plurality of partition nucleic acid barcode sequences or complements thereof.
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Abstract
The present disclosure provides methods, systems, and compositions for parallel processing of nucleic acid samples. Methods and systems of the present disclosure comprise the use of sample-specific barcode sequences, which facilitate the multiplexing of samples, detection of discrete cell populations within a pooled population, and detection of partitions comprising more than one cell.
118 Citations
33 Claims
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1. A method for analyzing cellular occupancy of partitions, comprising:
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(a) contacting a plurality of cells with a plurality of labelling molecules comprising a plurality of cell nucleic acid barcode sequences to generate a plurality of labelled cells, wherein each of said plurality of labelled cells comprises a different cell nucleic acid barcode sequence; (b) generating a plurality of partitions comprising said plurality of labelled cells and a plurality of beads, wherein said plurality of beads comprise a plurality of partition nucleic acid barcode sequences coupled thereto, wherein each of said plurality of partitions comprises a different partition nucleic barcode sequence, and wherein at least a fraction of said plurality of partitions comprises more than one labelled cell of said plurality of labelled cells; (c) within said plurality of partitions, (i) using partition nucleic acid barcode sequences of said plurality of partition nucleic acid barcode sequences and cell nucleic acid barcode sequences of said plurality of cell nucleic acid barcode sequences to synthesize a plurality of barcoded nucleic acid products, and (ii) releasing or recovering said plurality of barcoded nucleic acid products or derivatives thereof from said plurality of partitions; and (d) identifying-sequencing said plurality of barcoded nucleic acid products or derivatives thereof to determine that at least two labelled cells of said plurality of labelled cells originate from a same partition using (i) said cell nucleic acid barcode sequences of said plurality of cell nucleic acid barcode sequences or complements thereof and (ii) said partition nucleic acid barcode sequences of said plurality of partition nucleic acid barcode sequences or complements thereof. - View Dependent Claims (2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 31, 32)
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6. (canceled)
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26. (canceled)
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28. (canceled)
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30. A method for analyzing cellular occupancy of a partition, comprising:
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(a) labelling a first cell with a first cell nucleic acid barcode sequence and a second cell with a second cell nucleic acid barcode sequence to generate a first labelled cell and a second labelled cell, wherein said first cell nucleic acid barcode sequence has a different sequence than said second cell nucleic acid barcode sequence; (b) generating a partition comprising said first labelled cell and said second labelled cell, wherein said partition further comprises a plurality of partition nucleic acid barcode molecules coupled to a bead, wherein each of said plurality of partition nucleic acid barcode molecules comprises a partition nucleic acid barcode sequence; (c) within said partition, using said first cell nucleic acid barcode sequence, said second cell nucleic acid barcode sequence, and said plurality of partition nucleic acid barcode molecules to generate (i) a first barcoded nucleic acid molecule comprising said first cell nucleic acid barcode sequence or a complement thereof and said partition nucleic acid barcode sequence or a complement thereof, and (ii) a second barcoded nucleic acid molecule comprising said second cell nucleic acid barcode sequence or a complement thereof and said partition nucleic acid barcode sequence or a complement thereof, and (d) sequencing said first barcoded nucleic acid molecule and said second barcoded nucleic acid molecule, or a derivative of said first barcoded nucleic acid molecule or said second barcoded nucleic acid molecule, to (i) identify said first cell nucleic acid barcode sequence and said second cell nucleic acid barcode sequence, or a complement of said first cell nucleic acid barcode sequence or said second cell nucleic acid barcode sequence, thereby identifying said first labelled cell and said second labelled cell, and (ii) identify said partition nucleic acid barcode sequence or complement thereof, thereby identifying said first labelled cell and said second labelled cell as originating from said partition based on said first barcoded nucleic acid molecule and said second barcoded nucleic acid molecule having said partition nucleic acid barcode sequence or a complement thereof. - View Dependent Claims (33)
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Specification