Cell barcoding for single cell sequencing

A method of tagging cell-specific barcodes to cell nucleic acids, the method comprising,

• providing (i) cells or isolated cell nuclei having heterologous barcoded oligonucleotides attached to cell membranes of the cells or (ii) cell nuclei comprising heterologous oligonucleotides attached to nuclear membranes of the individual cell nuclei;
• mixing the cells or nuclei with a liquid-form hydrogel;
• cross-linking the hydrogel around the cells or nuclei, wherein the hydrogel forms a solid gel;
• releasing the heterologous barcoded oligonucleotides from the cell membranes or nuclear membranes to generate released heterologous barcoded oligonucleotides;
• allowing the heterologous barcoded oligonucleotides released from the cell membranes or nuclear membranes to locate at solidified hydrogel surrounding the cells or nuclei;
• attaching the heterologous barcoded oligonucleotides to cell polynucleotides or copies or cDNAs thereof to form barcoded cell polynucleotides;
• dissolving the solidified hydrogel or extracting the barcoded cell polynucleotides from the solidified hydrogel, thereby releasing barcoded cell polynucleotides from the hydrogel, thereby tagging cell-specific barcodes to cell nucleic acids.