Methods for spatial analysis using proximity ligation
OwnerDavid Michael Patterson, Sultan Doganay Tuncer +1inventors
InventorsDavid Michael Patterson, Sultan Doganay Tuncer, Zachary Bent
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Abstract
The present disclosure provides methods and compositions for detecting and spatially locating analyte interactions and gene expression in a biological sample. For example, provided herein are methods of determining a location of at least one analyte in a biological sample using analyte-binding moieties, proximity ligation, and an array including capture probes.
Claims35
A method of determining a location or abundance of an interaction between a first analyte and a second analyte in a biological sample, the method comprising:
- (a) contacting the biological sample with 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) attaching a first analyte-binding moiety to the first analyte, wherein the first analyte-binding moiety is bound to a first oligonucleotide comprising a first barcode that is unique to the interaction between the first analyte and the first analyte-binding moiety;
- (c) attaching a second analyte-binding moiety to the second analyte, wherein the second analyte-binding moiety is bound to a second oligonucleotide comprising a second barcode that is unique to the interaction between the second analyte and the second analyte-binding moiety;
- (d) hybridizing a third oligonucleotide to the first oligonucleotide and to the second oligonucleotide;
- (e) ligating the first oligonucleotide and the second oligonucleotide, thereby generating a ligation product comprising a capture probe capture domain sequence;
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- (f) hybridizing the capture probe capture domain sequence to the capture domain;
- and
- (g) determining (i) all or a portion of the sequence of the spatial barcode or a complement thereof;
- (ii) all or a portion of the sequence of the first barcode or a complement thereof;
- (iii) all or a portion of the sequence of the second barcode or a complement thereof;
- and using the determined sequences of (i), (ii), and (iii) to identify the location or abundance of the interaction between the first analyte and the second analyte in the biological sample.
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A method of determining a location or abundance of an interaction between a first analyte and a second analyte in a biological sample, the method comprising:
- (a) contacting the biological sample with 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) attaching a first analyte-binding moiety to the first analyte, wherein the first analyte-binding moiety is bound to a first oligonucleotide comprising a first barcode that is unique to the interaction between the first analyte and the first analyte-binding moiety and a first bridge sequence;
- (c) attaching a second analyte-binding moiety to the second analyte, wherein the second analyte-binding moiety is bound to a second oligonucleotide comprising a second barcode that is unique to the interaction between the second analyte and the second analyte-binding moiety and a second bridge sequence;
- (d) hybridizing the first bridge sequence to the second bridge sequence, thereby creating a hybridized proximity oligonucleotide comprising a capture probe capture domain sequence;
- (e) hybridizing the capture probe capture domain sequence to the capture domain;
- (f) determining (i) all or a portion of the sequence of the first barcode or a complement thereof;
- (ii) all or a portion of the sequence of the second barcode or a complement thereof, and (iii) all or a part of the sequence of the spatial barcode or a complement thereof, and using the determined sequence of (i), (ii), and (iii) to identify the location or abundance of the interaction between the first analyte and the second analyte in the biological sample.
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Dependencies are inferred from the claim text.