Spatially addressable molecular barcoding
AssigneeBecton, Dickinson and Company
InventorsStephen P. A. Fodor, Christina Fan, Glenn Fu, Geoffrey Facer
Life of this patent
Estimating the term…
Abstract
The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.
Claims43
A method for determining spatial locations of a plurality of single cells, comprising:
- stochastically barcoding the plurality of single cells using a plurality of synthetic particles,
- wherein each of the plurality of synthetic particles comprises a plurality of stochastic barcodes, a first group of optical labels, and a second group of optical labels,
- wherein each of the plurality of stochastic barcodes comprises a cellular label and a molecular label,
- wherein each optical label in the first group of optical labels comprises a first optical moiety and each optical label in the second group of optical labels comprises a second optical moiety, and
- wherein each of the plurality of synthetic particles is associated with an optical barcode comprising the first optical moiety and the second optical moiety;
- detecting the optical barcode of each of the plurality of synthetic particles to determine the location of each of the plurality of synthetic particles;
- and
- determining the spatial locations of the plurality of single cells based on the locations of the plurality of synthetic particles.
A synthetic particle composition, comprising:
- a synthetic particle;
- a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a cellular label and a molecular label;
- a first group of optical labels;
- and
- a second group of optical labels,
- wherein the plurality of stochastic barcodes, the first group of optical labels, and the second group of optical labels are attached to the surface of the synthetic particle,
- wherein each optical label in the first group of optical labels comprises a first optical moiety and each optical label in the second group of optical labels comprises a second optical moiety, and
- wherein each of the plurality of synthetic particles the synthetic particle is associated with an optical barcode comprising the first optical moiety and the second optical moiety.
A method for determining the number and spatial locations of a plurality of targets in a sample, comprising:
- providing a solid support comprising a plurality of synthetic particles associated with a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label;
- decoding the solid support by contacting the solid support with a plurality of decoding nucleic acids labeled with a decoding label and detecting the presence of the decoding label,
- wherein at least some portion of each of the plurality of stochastic barcodes is single stranded to allow hybridization to a decoding nucleic acid, and
- wherein decoding comprises two or more sequential hybridizations of decoding nucleic acids to each of the plurality of stochastic barcodes;
- stochastically barcoding the plurality of targets in the sample by hybridizing the plurality of stochastic barcodes with the plurality of targets to generate stochastically barcoded targets;
- identifying the spatial location of each of the plurality of targets by correlating the spatial labels of the plurality of the stochastic barcodes with the spatial locations of the plurality of targets in the sample;
- and
- estimating the number of each of the plurality of targets by determining sequences of the spatial labels and molecular labels of the plurality of the stochastic labels and counting the number of the molecular labels with distinct sequences.
Dependencies are inferred from the claim text.