A method for de-crosslinking a fixed biological sample for determining the location of a target nucleic acid in the fixed biological sample, the method comprising: (a) providing a spatial array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (b) de-crosslinking one or more crosslinks in the fixed biological sample, wherein the de-crosslinking comprises heating the fixed biological sample such that the capture domain hybridizes to a proxy of the target nucleic acid; (c) contacting the fixed biological sample with: (i) a first probe, wherein the first probe comprises in a 5' to 3' direction: a first functional domain and a first sequence that is substantially complementary to a portion of the target nucleic acid, and (ii) a second probe, wherein the second probe comprises in a 5' to 3' direction: a 5' phosphate, a second sequence that is substantially complementary to a portion of the target nucleic acid and a capture sequence that is substantially complementary to the capture domain of the capture probe; (d) hybridizing the first probe and the second probe to the target nucleic acid and ligating the 3' end of the first probe to the 5' end of the second probe to generate the proxy of the target nucleic acid; (e) hybridizing the proxy of the target nucleic acid to the capture domain of the capture probe, extending the capture probe using the proxy as a template thereby generating an extended capture probe, and generating a second strand hybridized to the extended capture probe, wherein the second strand comprises a sequence complementary to the spatial barcode and the proxy of the target nucleic acid; and (f) determining (i) the sequence of the spatial barcode, or a complement thereof, and (ii) all or a portion of the proxy of the target nucleic acid, or a complement thereof, and using the determined sequences of (i) and (ii) to identify the location of the target nucleic acid in the fixed biological sample. (a) providing a spatial array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (b) de-crosslinking one or more crosslinks in the fixed biological sample, wherein the de-crosslinking comprises heating the fixed biological sample such that the capture domain hybridizes to a proxy of the target nucleic acid; (c) contacting the fixed biological sample with: (i) a first probe, wherein the first probe comprises in a 5' to 3' direction: a first functional domain and a first sequence that is substantially complementary to a portion of the target nucleic acid, and (ii) a second probe, wherein the second probe comprises in a 5' to 3' direction: a 5' phosphate, a second sequence that is substantially complementary to a portion of the target nucleic acid and a capture sequence that is substantially complementary to the capture domain of the capture probe; (i) a first probe, wherein the first probe comprises in a 5' to 3' direction: a first functional domain and a first sequence that is substantially complementary to a portion of the target nucleic acid, and (ii) a second probe, wherein the second probe comprises in a 5' to 3' direction: a 5' phosphate, a second sequence that is substantially complementary to a portion of the target nucleic acid and a capture sequence that is substantially complementary to the capture domain of the capture probe; (d) hybridizing the first probe and the second probe to the target nucleic acid and ligating the 3' end of the first probe to the 5' end of the second probe to generate the proxy of the target nucleic acid; (e) hybridizing the proxy of the target nucleic acid to the capture domain of the capture probe, extending the capture probe using the proxy as a template thereby generating an extended capture probe, and generating a second strand hybridized to the extended capture probe, wherein the second strand comprises a sequence complementary to the spatial barcode and the proxy of the target nucleic acid; and (f) determining (i) the sequence of the spatial barcode, or a complement thereof, and (ii) all or a portion of the proxy of the target nucleic acid, or a complement thereof, and using the determined sequences of (i) and (ii) to identify the location of the target nucleic acid in the fixed biological sample.