Methods for spatial analysis using targeted RNA depletion

A method for depleting an undesirable RNA molecule in a biological sample on a spatial array, the method comprising:

• (a) providing the biological sample on the spatial array, wherein the spatial array comprises a plurality of attached capture probes, wherein a capture probe of the plurality of capture probes comprises (i) a spatial barcode and (ii) a capture domain that is substantially complementary to an analyte of a plurality of analytes in the biological sample;
• (b) adding a plurality of undesirable RNA depletion probes to the biological sample, wherein an undesirable RNA depletion probe of the plurality of undesirable RNA depletion probes comprises a sequence that is substantially complementary to a sequence of the undesirable RNA molecule;
• (c) hybridizing the undesirable RNA depletion probe to the undesirable RNA molecule, thereby generating an undesirable RNA depletion probe-undesirable RNA molecule complex;
• and
• (d) removing the undesirable RNA depletion probe-undesirable RNA molecule complex to deplete the undesirable RNA molecule in the biological sample on the spatial array.