Methods for in situ transcriptomics and proteomics

A method of sequencing, said method comprising

• contacting a cell or tissue comprising a nucleic acid molecule with a polynucleotide probe comprising a first target hybridization sequence and a second target hybridization sequence;
• hybridizing the first target hybridization sequence to the nucleic acid molecule and hybridizing the second target hybridization sequence to the nucleic acid molecule;
• ligating the first target hybridization sequence to the second target hybridization sequence to form a circular polynucleotide;
• amplifying the circular polynucleotide to form an amplification product;
• and
• hybridizing a first sequencing primer to the amplification product, and sequencing the first target hybridization sequence or the second target hybridization sequence.

A method of detecting a gene sequence, said method comprising:

• contacting a cell or tissue comprising a first nucleic acid molecule comprising the gene sequence with a first polynucleotide probe comprising a first target hybridization sequence and a second target hybridization sequence;
• hybridizing the first target hybridization sequence to the first nucleic acid molecule and hybridizing the second target hybridization sequence to the first nucleic acid molecule;
• ligating the first target hybridization sequence to the second target hybridization sequence to form a first circular polynucleotide;
• contacting the cell or tissue comprising a second nucleic acid molecule comprising the gene sequence with a second polynucleotide probe comprising a third target hybridization sequence and a fourth target hybridization sequence;
• hybridizing the third target hybridization sequence to the second nucleic acid molecule and hybridizing the fourth target hybridization sequence to the second nucleic acid molecule;
• ligating the third target hybridization sequence to the fourth target hybridization sequence to form a second circular polynucleotide;
• amplifying the first circular polynucleotide to form a first amplification product and amplifying the second circular polynucleotide to form a second amplification product;
• hybridizing a first sequencing primer to the first amplification product, and sequencing the first target hybridization sequence or the second target hybridization sequence;
• and
• hybridizing a second sequencing primer to the second amplification product, and sequencing the third target hybridization sequence or the fourth target hybridization sequence.