Methods of detecting analytes
AssigneeSpatial Transcriptomics AB
InventorsJonas Frisen, Patrik Stahl, Joakim Lundeberg
Life of this patent
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Abstract
Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3′ end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3′ of the positional domain.
Claims30
A method for determining the location of a nucleic acid in a tissue section comprising:
- a) providing a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises:
- (i) a capture domain that binds the nucleic acid, and
- (ii) a positional domain comprising a nucleotide sequence, wherein the nucleotide sequence of each of the positional domains is unique to a distinct position in the substrate;
- b) contacting the tissue section with the substrate;
- c) releasing the capture probe from the substrate;
- d) extending a 3′ end of the capture probe using the nucleic acid of the tissue section bound to the capture domain as a template to generate an extended nucleic acid product;
- and
- e) determining (i) all or a part of the nucleotide sequence of the nucleic acid of the tissue section bound to the capture domain, or a complement thereof, and (ii) the nucleotide sequence of the positional domain, or a complement thereof, wherein the nucleotide sequences of (i) and (ii) indicate the nucleic acid was obtained from the tissue section at a distinct position on the substrate by the capture probe, thereby determining the location of the nucleic acid in the tissue section.
A method for determining the location of a nucleic acid in a tissue section comprising:
- a) providing a substrate comprising a plurality capture probes, wherein a capture probe of the plurality of capture probe comprises:
- (i) a capture domain that binds a nucleic acid, and
- (ii) a positional domain comprising a nucleotide sequence, wherein the nucleotide sequence of each of the positional domains is unique to a distinct position in the substrate;
- b) contacting a tissue section with the substrate;
- c) imaging one or more fluorescent marker probes;
- d) releasing the capture probe from the substrate;
- e) extending a 3′ end of the capture probe using the nucleic acid of the tissue section bound to the capture domain as a template to generate an extended nucleic acid product;
- and
- f) determining (i) all or a part of the nucleotide sequence of the nucleic acid of the tissue section bound to the capture domain, or a complement thereof, and (ii) the nucleotide sequence of the positional domain, or a complement thereof, wherein the nucleotide sequences of (i) and (ii) indicate the nucleic acid was obtained from the tissue section at a distinct position on the substrate by the capture probe, thereby determining the location of the nucleic acid in the tissue section.
Dependencies are inferred from the claim text.