Patent ID: 11926822
Assignee: 10X GENOMICS, INC.
Field: Biotechnology (Chemistry)
Classification: CPC C | IPC C

Claim 9:
10. A method for determining a location of a nucleic acid in a tissue sample in a three dimensional space, the method comprising:
(a) placing the tissue sample on an array and immobilizing the tissue sample by adding a hydrogel matrix to the tissue sample on the array, wherein the hydrogel matrix comprises a polymer;
(b) adding a plurality of pairs of spatially-programmed capture probes to the hydrogel matrix, wherein a pair of spatially-programmed capture probes in the plurality of pairs of spatially-programmed capture probes comprises a first spatially-programmed capture probe and a second spatially-programmed capture probe, wherein:
the first and the second spatially-programmed capture probe comprises a detectable moiety;
and
each of the first spatially-programmed capture probe and the second spatially-programmed capture probe comprise a programmable migration domain that migrates to a z-axis location in the tissue sample,

(c) migrating the pair of spatially-programmed capture probes comprising the detectable moiety into the hydrogel matrix from a surface of the hydrogel matrix that is distal to a surface of the hydrogel matrix;
(d) hybridizing the first spatially-programmed capture probe and the second spatially-programmed capture probe to the nucleic acid;
(e) ligating the first spatially-programmed capture probe and the second spatially-programmed capture probe to generate a ligation product;
(f) detecting the z-axis location of the detectable moiety in the tissue sample, thereby determining the z-axis location of the ligation product in the tissue sample;
(g) migrating the ligation product to the array, wherein the array comprises a plurality of affixed capture probes, wherein an affixed capture probe of the plurality of affixed capture probes comprises a spatial barcode and a capture domain that hybridizes to a sequence in the ligation product; and
(h) determining (i) a sequence of the ligation product, or a complement thereof, and (ii) the sequence of the spatial barcode, or a complement thereof, and using the determined sequences of (i) and (ii), and the determined z-axis location of the detectable moiety in (f), to identify a three-dimensional location of the nucleic acid in the tissue sample.