Methods for determining a location of an analyte in a biological sample

Abstract

Provided herein are methods of determining a location of a target analyte in a non-permeabilized biological sample that include the use of a blocking probe.

What is claimed is: 
     
         1 . A method for determining a location of a target nucleic acid in a biological sample, the method comprising:
 (a) disposing a non-permeabilized biological sample onto an array at a first area, wherein the array comprises a plurality of capture probes, wherein:   the first area comprises a capture probe of the plurality of capture probes comprising (i) a spatial barcode and (ii) a capture domain; and   a second area of the array comprises a capture probe of the plurality of capture probes comprising (i) a spatial barcode and (ii) a capture domain, and the second area is adjacent to the biological sample disposed on the array;   (b) contacting the second area of the array with a solution comprising a blocking probe, wherein the blocking probe comprises a sequence that binds specifically to the capture domain of the capture probe in the second area of the array;   (c) removing residual solution comprising the blocking probe from the second area of the array;   (d) permeabilizing the biological sample, such that the capture domain of the capture probe of the first area of the array binds specifically to the target nucleic acid; and   (e) determining (i) a sequence corresponding to the spatial barcode of the capture probe of the first area of the array, or a complement thereof, and (ii) all or a portion of a sequence corresponding to the target nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the target nucleic acid in the biological sample.