Solid state single cell method for analyzing fixed biological cells

A method of analysis for aldehyde fixed nuclei comprising:

• providing a substrate comprising a plurality of capture regions, wherein a capture region of the plurality of capture regions comprises:
• a plurality of ligands and
• a plurality of barcode molecules, wherein a barcode molecule of the plurality of barcode molecules comprises a common barcode sequence and a nucleic acid binding sequence;
• contacting a plurality of aldehyde fixed nuclei with the substrate, wherein an aldehyde fixed nuclei of the plurality of aldehyde fixed nuclei binds to a ligand of the plurality of ligands, thereby generating a captured aldehyde fixed nuclei at the capture region;
• applying a coating to the substrate prior to reversing fixation, thereby immobilizing the captured aldehyde fixed nuclei;
• reversing fixation of the aldehyde captured fixed nuclei at the capture region to release a plurality of nucleic acids from the captured aldehyde fixed nuclei and hybridizing a nucleic acid of the plurality of nucleic acids to the nucleic acid binding sequence of the barcode molecule;
• and
• generating a plurality of barcoded molecules from the plurality of nucleic acids and the plurality of barcode molecules, wherein a barcoded molecule of the plurality of barcoded molecules comprises the common barcode sequence, or a complement thereof, and a sequence corresponding to the nucleic acid, or a complement thereof.