Matrix imprinting and clearing

A method, comprising:

• exposing a sample comprising nucleic acid targets to a plurality of MERFISH nucleic acid probes comprising a target binding sequence and one or more read sequences;
• exposing a sample to a plurality of anchor nucleic acid probes, wherein the anchor probes specifically hybridize to the nucleic acid targets;
• embedding at least a portion of the sample within a polyacrylamide gel;
• immobilizing at least some of the anchor nucleic acid probes to the polyacrylamide gel;
• clearing proteins and/or lipids and/or DNA and/or extracellular matrix and/or RNA molecules from the sample;
• and
• determining binding of the MERFISH nucleic acid probes to the nucleic acid targets by imaging the polyacrylamide gel wherein the MERFISH probes are contacted with a plurality of secondary nucleic acid probes comprising a fluorescent dye and a recognition sequence that hybridizes to the one or more read sequence of the MERFISH probe.

A method for anchoring target mRNA transcripts within a matrix, clearing non-target cellular components and imaging the target mRNA, comprising:

• exposing a sample comprising a cell or a tissue to a plurality of anchor probes and a plurality of primary probes, wherein the anchor probes comprise a moiety that is complementary and hybridizes to the target mRNA transcript and a moiety that covalently binds to the matrix, and wherein the primary probes do not comprise a fluorescent label;
• polymerizing a polymer matrix within the sample;
• anchoring the target mRNA transcript to the polymer matrix wherein the anchor probe covalently binds the polymer matrix;
• clearing the non-target cellular components from the polymer matrix wherein the target mRNA transcripts remain anchored in the polymer matrix;
• and,
• contacting the primary nucleic acid probes with a plurality of secondary nucleic acid probes comprising a fluorescent dye and a recognition sequence that hybridizes to a read sequence of the primary nucleic acid probe and imaging.