Patent ID: 11959075
Assignee: PRESIDENT AND FELLOWS OF HARVARD COLLEGE
Field: Biotechnology (Chemistry)
Classification: CPC C  G | IPC C  G

Claim 0:
1. A method for imaging RNA spatial organization in a sample comprising:
a. contacting the sample comprising a plurality of distinct RNA species in situ with a plurality of primary nucleic acid probe pools each of the nucleic acid probes comprising a target sequence and one or more read sequences, wherein each pool of nucleic acid probes hybridize to a distinct RNA species and each pool of probes encode a N-bit codeword with a Hamming weight of at least 2 that was assigned to each distinct RNA species, wherein each assigned N-bit codeword is a valid codeword with a Hamming distance equal to or greater than 2 between valid codewords and wherein each of the read sequences correspond to a bit value of 1 for the codewords assigned to the distinct RNA species;
b. contacting the bound primary nucleic acid probes with a plurality of readout probes comprising a fluorescent label, wherein the readout probes hybridize to the read sequences of the primary nucleic probes;
c. imaging the readout probes bound to the primary nucleic acid probes; and,
d. repeating steps b) and c) in one or more sequential hybridization and imaging rounds until all N positions in the N-bit codeword have been imaged providing an imaged codeword corresponding to each distinct RNA species in a spatial organization.