Sequence based imaging
OwnerColin THOMinventor
Life of this patent
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Abstract
Described herein are a variety of method, reagents and kits for determining and/or representing the spatial relationships of oligonucleotide probes (or probe targets) in a biological sample. Such representation may take the form of encoding spatial relationships in oligonucleotide sequences of reaction products, sequencing of spatially encoded reaction products, and analyzing or visualizing spatial relationships based on the spatially encoded sequences.
Claims20
A method of representing the spatial relationships of oligonucleotide probes in a biological sample, the method comprising:
- a) contacting a biological sample with a set of oligonucleotide probes;
- and
- b) forming reaction products in the biological sample;
- wherein the reaction products are formed between proximal oligonucleotide probes comprising different variable sequences;
- wherein a plurality of the oligonucleotide probes are target-specific oligonucleotide probes;
- wherein the reaction products that encode the proximity of a plurality of oligonucleotide probes;
- wherein the variable sequences of a single oligonucleotide probe are present on a plurality of different reaction products,
- wherein one or more of the reaction products comprise a different combination of variable sequences;
- and
- wherein one or more of the reaction products comprise variable sequences from at least 3 different oligonucleotide probes.
A kit for encoding spatial relationships of targets in a biological sample, the kit comprising:
- a set of oligonucleotide probes, wherein one or more of the probes in the set are target specific oligonucleotide probes;
- wherein one or more oligonucleotide probes in the kit comprise a first complimentary sequence at the 3′ end that hybridizes to other oligonucleotide probes in the set;
- and wherein extending from the first hybridization sequence encodes one or more identifiers of the template oligonucleotide probe and terminates in a second hybridization sequence that can hybridize to, and extend along, another oligonucleotide probe in the set.
Dependencies are inferred from the claim text.