Methods, compositions, and systems for detecting exogenous nucleic acids
Assignee10x Genomics, Inc.
InventorsHardeep Pal Singh, Augusto Manuel Tentori
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Abstract
Provided herein are methods for capturing an exogenous probe and/or a capture handle sequence to a capture domain of a capture probe. Compositions, systems, and kits also are disclosed. In some instances, the methods include detecting an exogenous nucleic acid in a biological sample by hybridizing a first exogenous probe oligonucleotide and a second exogenous probe oligonucleotide to an exogenous nucleic acid in a biological sample on a first substrate, coupling the exogenous probe oligonucleotides, and capturing the coupled exogenous probe on a spatial array.
Claims20
A method of detecting an exogenous nucleic acid in a biological sample, the method comprising:
- (a) hybridizing a first exogenous probe oligonucleotide and a second exogenous probe oligonucleotide to an exogenous nucleic acid in a biological sample on a first substrate, wherein the first exogenous probe oligonucleotide and the second exogenous probe oligonucleotide each comprise a sequence that is substantially complementary to a first sequence and a second sequence of the exogenous nucleic acid, respectively, and wherein the second exogenous probe oligonucleotide comprises an exogenous capture probe binding domain;
- (b) coupling the first exogenous probe oligonucleotide and the second exogenous probe oligonucleotide, thereby generating an exogenous connected probe;
- (c) aligning the first substrate with a second substrate comprising an array, such that at least a portion of the biological sample is aligned with at least a portion of the array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises:
- (i) a spatial barcode and (ii) a capture domain;
- (d) releasing the exogenous connected probe from the exogenous nucleic acid when the biological sample is aligned with at least a portion of the array;
- and
- (e) hybridizing the exogenous capture probe binding domain of the exogenous connected probe to the capture domain of the capture probe.
A method of detecting an exogenous nucleic acid in a biological sample, the method comprising:
- (a) hybridizing a first exogenous probe oligonucleotide and a second exogenous probe oligonucleotide to an exogenous nucleic acid in a biological sample on a first substrate, wherein the first exogenous probe oligonucleotide and the second exogenous probe oligonucleotide each comprise a sequence that is substantially complementary to a first sequence and a second sequence of the exogenous nucleic acid, respectively, and wherein the second exogenous probe oligonucleotide comprises an exogenous capture probe binding domain;
- (b) coupling the first exogenous probe oligonucleotide and the second exogenous probe oligonucleotide, thereby generating an exogenous connected probe;
- (c) aligning the first substrate with a second substrate comprising an array, such that at least a portion of the biological sample is aligned with at least a portion of the array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises:
- (i) a spatial barcode and (ii) a capture domain;
- (d) releasing the capture probe from the array when the biological sample is aligned with at least a portion of the array;
- and
- (e) hybridizing the exogenous capture probe binding domain of the exogenous connected probe to the capture domain of the capture probe.
Dependencies are inferred from the claim text.