A method of uniquely labeling RNA molecules within a plurality of cells, the method comprising: (a) fixing and permeabilizing a first plurality of cells prior to step (b), wherein the first plurality of cells are fixed and permeabilized at 4 °C or below 4 °C; (b) reverse transcribing the RNA molecules within the first plurality of cells to form complementary DNA (cDNA) molecules within the first plurality of cells, wherein reverse transcribing the RNA molecules comprises coupling primers to the RNA molecules, wherein the primers comprise at least one of a poly sequence or a random sequence; (c) dividing the first plurality of cells comprising cDNA molecules into at least two primary aliquots, the at least two primary aliquots comprising a first primary aliquot and a second primary aliquot; (d) providing primary nucleic acid tags to the at least two primary aliquots, wherein the primary nucleic acid tags provided to the first primary aliquot are different from the primary nucleic acid tags provided to the second primary aliquot; (e) coupling the cDNA molecules within each of the at least two primary aliquots with the provided primary nucleic acid tags; (f) combining the at least two primary aliquots; (g) dividing the combined primary aliquots into at least two secondary aliquots, the at least two secondary aliquots comprising a first secondary aliquot and a second secondary aliquot; (h) providing secondary nucleic acid tags to the at least two secondary aliquots, wherein the secondary nucleic acid tags provided to the first secondary aliquot are different from the secondary nucleic acid tags provided to the second secondary aliquot; (i) coupling the cDNA molecules within each of the at least two secondary aliquots with the provided secondary nucleic acid tags; (j) combining final aliquots; (k) lysing the first plurality of cells to release the cDNA molecules from within the first plurality of cells to form a lysate; and (l) adding a protease inhibitor and a binding agent to the lysate such that the cDNA molecules bind the binding agent. (a) fixing and permeabilizing a first plurality of cells prior to step (b), wherein the first plurality of cells are fixed and permeabilized at 4 °C or below 4 °C; (b) reverse transcribing the RNA molecules within the first plurality of cells to form complementary DNA (cDNA) molecules within the first plurality of cells, wherein reverse transcribing the RNA molecules comprises coupling primers to the RNA molecules, wherein the primers comprise at least one of a poly sequence or a random sequence; (c) dividing the first plurality of cells comprising cDNA molecules into at least two primary aliquots, the at least two primary aliquots comprising a first primary aliquot and a second primary aliquot; (d) providing primary nucleic acid tags to the at least two primary aliquots, wherein the primary nucleic acid tags provided to the first primary aliquot are different from the primary nucleic acid tags provided to the second primary aliquot; (e) coupling the cDNA molecules within each of the at least two primary aliquots with the provided primary nucleic acid tags; (f) combining the at least two primary aliquots; (g) dividing the combined primary aliquots into at least two secondary aliquots, the at least two secondary aliquots comprising a first secondary aliquot and a second secondary aliquot; (h) providing secondary nucleic acid tags to the at least two secondary aliquots, wherein the secondary nucleic acid tags provided to the first secondary aliquot are different from the secondary nucleic acid tags provided to the second secondary aliquot; (i) coupling the cDNA molecules within each of the at least two secondary aliquots with the provided secondary nucleic acid tags; (j) combining final aliquots; (k) lysing the first plurality of cells to release the cDNA molecules from within the first plurality of cells to form a lysate; and (l) adding a protease inhibitor and a binding agent to the lysate such that the cDNA molecules bind the binding agent.