Methods for spatial analysis using targeted rna depletion

Abstract

Provided herein are methods for spatial analysis using targeted RNA depletion.

What is claimed is: 
     
         1 . A method for identifying a location of an analyte in a biological sample, the method comprising:
 (a) contacting a biological sample with a first probe oligonucleotide, a second probe oligonucleotide, and a plurality of undesirable RNA depletion probes, wherein the first probe oligonucleotide and the second probe oligonucleotide are substantially complementary to adjacent sequences of the analyte, wherein the second probe oligonucleotide comprises a capture probe binding domain that is capable of binding to a capture domain of a capture probe, and wherein an undesirable RNA depletion probe of the plurality of undesirable RNA depletion probes is substantially complementary to a sequence of an undesirable RNA molecule in the biological sample;   (b) hybridizing the first probe oligonucleotide and the second probe oligonucleotide to the analyte;   (c) hybridizing the undesirable RNA depletion probe to the undesirable RNA molecule;   (d) ligating the first probe oligonucleotide and the second probe oligonucleotide, thereby creating a ligated probe that is substantially complementary to the analyte;   (e) removing the plurality of undesirable RNA depletion probe-undesirable RNA complexes and releasing the ligated probe from the analyte;   (f) hybridizing the capture probe binding domain of the ligated probe to a capture domain of a capture probe that is affixed to the substrate; and   (g) determining (i) all or a part of the sequence of the ligated probe specifically bound to the capture domain, or a complement thereof, and (ii) all or a part of the sequence of the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to identify the location of the analyte in the biological sample.