Sample indexing for single cells
First Claim
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1. A method, comprising:
- (a) contacting a first sample comprising a first plurality of cells and a second sample comprising a second plurality of cells with a first sample indexing composition and a second sample indexing composition, respectively, to form a first labeled sample and a second labeled sample, respectively, each comprising cells associated with the first sample indexing composition and the second sample indexing composition, respectively,wherein the first sample indexing composition comprises a first cellular component binding reagent associated with a first sample indexing oligonucleotide, wherein the first cellular component binding reagent is capable of specifically binding to a cellular component target of each of the first plurality of cells,wherein the second sample indexing composition comprises a second cellular component binding reagent associated with a second sample indexing oligonucleotide, wherein the second cellular component binding reagent is capable of specifically binding to a cellular component target of each of the second plurality of cells,wherein the first and second sample indexing oligonucleotides comprise a first sample indexing sequence and a second sample indexing sequence, respectively, and wherein the first sample indexing sequence and the second sample indexing sequence comprise different sequences, andwherein the cellular component target of each of the first plurality of cells and the cellular component target of each of the second plurality of cells are the same;
(b) pooling the first labeled sample and the second labeled sample to form a combined labeled sample comprising cells associated with the first sample indexing composition and cells associated with the second sample indexing composition, respectively;
(c) partitioning the cells associated with the first sample indexing composition and the cells associated with the second sample indexing composition of the combined labeled sample to a plurality of partitions, wherein the partitions of the plurality of partitions each comprises a single cell of the combined labeled sample;
(d) subjecting the first sample indexing oligonucleotide or the second sample indexing oligonucleotide to one or more reactions to generate a first barcoded sample indexing oligonucleotide comprising the first sample indexing sequence, or a complement thereof, or a second barcoded sample indexing oligonucleotide comprising the second sample indexing sequence, or a complement thereof;
(e) obtaining sequencing information of the first barcoded sample indexing oligonucleotide or a second barcoded sample indexing oligonucleotide, or a portion thereof; and
(f) determining cells in the combined labeled sample is from the first sample or the second sample based on the first sample indexing sequence or the second sample indexing sequence, respectively, a complementary sequence thereof, or a portion thereof, in the sequence information obtained in (e).
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Abstract
Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.
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Citations
29 Claims
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1. A method, comprising:
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(a) contacting a first sample comprising a first plurality of cells and a second sample comprising a second plurality of cells with a first sample indexing composition and a second sample indexing composition, respectively, to form a first labeled sample and a second labeled sample, respectively, each comprising cells associated with the first sample indexing composition and the second sample indexing composition, respectively, wherein the first sample indexing composition comprises a first cellular component binding reagent associated with a first sample indexing oligonucleotide, wherein the first cellular component binding reagent is capable of specifically binding to a cellular component target of each of the first plurality of cells, wherein the second sample indexing composition comprises a second cellular component binding reagent associated with a second sample indexing oligonucleotide, wherein the second cellular component binding reagent is capable of specifically binding to a cellular component target of each of the second plurality of cells, wherein the first and second sample indexing oligonucleotides comprise a first sample indexing sequence and a second sample indexing sequence, respectively, and wherein the first sample indexing sequence and the second sample indexing sequence comprise different sequences, and wherein the cellular component target of each of the first plurality of cells and the cellular component target of each of the second plurality of cells are the same; (b) pooling the first labeled sample and the second labeled sample to form a combined labeled sample comprising cells associated with the first sample indexing composition and cells associated with the second sample indexing composition, respectively; (c) partitioning the cells associated with the first sample indexing composition and the cells associated with the second sample indexing composition of the combined labeled sample to a plurality of partitions, wherein the partitions of the plurality of partitions each comprises a single cell of the combined labeled sample; (d) subjecting the first sample indexing oligonucleotide or the second sample indexing oligonucleotide to one or more reactions to generate a first barcoded sample indexing oligonucleotide comprising the first sample indexing sequence, or a complement thereof, or a second barcoded sample indexing oligonucleotide comprising the second sample indexing sequence, or a complement thereof; (e) obtaining sequencing information of the first barcoded sample indexing oligonucleotide or a second barcoded sample indexing oligonucleotide, or a portion thereof; and (f) determining cells in the combined labeled sample is from the first sample or the second sample based on the first sample indexing sequence or the second sample indexing sequence, respectively, a complementary sequence thereof, or a portion thereof, in the sequence information obtained in (e). - 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)
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Specification