Spatially addressable molecular barcoding
AssigneeCellular Research, Inc.
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.
Claims26
A method for determining the numbers and spatial locations of a plurality of targets in a plurality of spatially ordered cells of a sample, comprising:
- associating cells of the plurality of spatially ordered cells at two or more spatial locations with a plurality of stochastic barcodes,
- wherein each stochastic barcode of the plurality of stochastic barcodes comprises a spatial label and a molecular label, and
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying the two or more spatial locations of the cells;
- stochastically barcoding the plurality of targets in the cells of the plurality of spatially ordered cells using the plurality of stochastic barcodes comprising the two or more different spatial labels for identifying the two or more spatial locations of the cells;
- estimating the numbers of the plurality of targets in the cells of the plurality of spatially ordered cells at the two or more spatial locations using the molecular labels of the plurality of stochastic barcodes;
- and
- identifying the spatial locations of the plurality of targets in the cells of the plurality of spatially ordered cells at the two or more spatial locations using the two or more different spatial labels of the plurality of stochastic barcodes.
A method for determining spatial locations of a plurality of targets in a plurality of spatially ordered cells of a sample, comprising:
- associating cells of the plurality of spatially ordered cells at two or more spatial locations with a plurality of stochastic barcodes,
- wherein each stochastic barcode of the plurality of stochastic barcodes comprises a spatial label, and
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying the two or more spatial locations of the cells;
- stochastically barcoding the plurality of targets in the cells of the plurality of spatially ordered cells using the plurality of stochastic barcodes comprising the two or more different spatial labels for identifying the two or more spatial locations of the cells;
- and
- identifying the spatial locations of the plurality of targets using the two or more different spatial labels.
A method for determining spatial locations of a plurality of targets in a plurality of spatially ordered cells of a sample, comprising:
- associating cells of the plurality of spatially ordered cells at two or more spatial locations with a plurality of stochastic barcodes,
- wherein each stochastic barcode of the plurality of stochastic barcodes comprises a spatial label and a molecular label, and
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying the two or more spatial locations of the cells;
- stochastically barcoding the plurality of targets in the cells of the plurality of spatially ordered cells using the plurality of stochastic barcodes comprising the two or more different spatial labels for identifying the two or more spatial locations of the cells, wherein each of the plurality of stochastic barcodes comprises a pre-spatial label;
- concatenating one or more spatial label blocks onto the pre-spatial label to generate a spatial label of the two or more different spatial labels;
- and
- identifying the spatial locations of the plurality of targets in the cells of the plurality of spatially ordered cells at the two or more spatial locations using the two or more different spatial labels of the plurality of stochastic barcodes.
A method for determining spatial locations of a plurality of targets in a plurality of spatially ordered cells of a sample, comprising:
- associating cells of the plurality of spatially ordered cells at two or more spatial locations with a plurality of stochastic barcodes,
- wherein each stochastic barcode of the plurality of stochastic barcodes comprises a spatial label and a molecular label, and
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying the two or more spatial locations of the cells;
- imaging the sample to generate a sample image;
- stochastically barcoding the plurality of targets in the cells of the plurality of spatially ordered cells using the plurality of stochastic barcodes comprising the two or more different spatial labels for identifying the two or more spatial locations of the cells;
- and
- identifying the spatial locations of the plurality of targets on the sample image using the two or more spatial labels.
A method for distinguishing a plurality of spatially ordered cells of two or more samples, comprising:
- associating cells of the plurality of spatially ordered cells at two or more spatial locations with a plurality of stochastic barcodes,
- wherein each stochastic barcode of the plurality of stochastic barcodes comprises a spatial label and a molecular label, and
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying the two or more spatial locations of the cells;
- stochastically barcoding a plurality of targets in the cells of plurality of spatially ordered cells using the plurality of stochastic barcodes comprising the two or more different spatial labels for identifying the two or more spatial locations of the cells;
- estimating the number of the plurality of targets in the cells of the plurality of spatially ordered cells at the two or more spatial locations using the molecular labels of the stochastic barcodes;
- and
- distinguishing the cells of the plurality of spatially ordered cells of the two or more samples from each other using the two or more different spatial labels.
A kit comprising:
- a plurality of stochastic barcodes,
- wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label,
- wherein the plurality of stochastic barcodes comprises two or more different spatial labels for identifying unique spatial locations of cells of a plurality of spatially ordered cells,
- and
- instructions for using the plurality of stochastic barcodes.
Dependencies are inferred from the claim text.