Methods of using master / copy arrays for spatial detection
Assignee10x Genomics, Inc.
InventorPreyas Shah
Life of this patent
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Abstract
This disclosure provides methods for spatial profiling of biological analytes present in a biological sample. Methods include generating feature arrays using a master/copy format using recessed arrays, and methods for using such arrays. For example spatially-tagged analyte capture analytes can be used in spatial detection in methods to determine the location of analytes (e.g., proteins) in biological samples.
Claims28
A method of generating an array, the method comprising:
- providing a substrate comprising a plurality of wells, a well of the plurality of wells comprising a recessed surface;
- applying a mask to one or more regions of the substrate that do not correspond to the plurality of wells;
- and
- applying a plurality of capture probes to the well, wherein a capture probe of the plurality of capture probes comprises a barcode unique to the well, such that one end of the capture probe is immobilized on the recessed surface of the well.
-15. (canceled)
An array of capture probes on a substrate, the array comprising:
- a substrate comprising a plurality of wells, a well of the plurality of wells comprising a recessed surface having a plurality of immobilized capture probes, wherein the plurality of immobilized capture probes comprises a total of between about 10,000 and about 300,000 capture probes, and wherein a capture probe of the plurality of immobilized capture probes comprises a barcode unique to the well, and wherein the well has a maximum cross-sectional dimension measured in a plane defined by the surface of the substrate of about 0.5 μm to about 10 μm.
-27. (canceled)
A method of generating an array of features on a substrate, the method comprising:
- providing a first substrate comprising a plurality of wells, a well of the plurality of wells comprising a recessed surface having a plurality of immobilized tagging probes wherein a tagging probe of the plurality of immobilized tagging probes comprises a spatial barcode unique to the well;
- depositing a feature in the well;
- copying the tagging probe onto the feature in the well, thereby generating a capture probe on the feature;
- transferring the feature in the well to a second substrate, and
- immobilizing the feature on the second substrate, thereby generating an array of the features on the second substrate.
-43. (canceled)
A method of identifying a location of a biological analyte in a biological sample comprising:
- (a) providing a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain;
- (b) contacting the substrate with a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises an analyte binding moiety and a capture agent barcode domain, and the capture probe binds to the analyte capture agent via the capture domain of the capture probe;
- (c) producing a spatially-tagged analyte capture agent, by extending the capture agent barcode domain to include a sequence that is complementary to the spatial barcode of the capture probe;
- (d) labelling a cell of the biological sample with one or more spatially-tagged analyte capture agents, by contacting the one or more spatially-tagged analyte capture agents with the biological sample, wherein at least one spatially-tagged analyte capture agent interacts with the biological analyte within the biological sample, and denaturing the spatially-tagged analyte capture agent from the capture probe;
- (e) dissociating the biological sample into a plurality of cells, wherein the at least one spatially-tagged analyte capture agent is associated with a dissociated cell;
- and
- (f) using the at least one spatially-tagged analyte capture agent to identify the location of the target biological analyte in the biological sample.
-50. (canceled)
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Dependencies are inferred from the claim text.