Methods, systems, and kits for detection of nucleic acid molecules

Abstract

The present disclosure provides methods, systems, and kits for processing or analyzing a sample. Processing a sample may comprise hybridizing a probe molecule to a binding region of a nucleic acid molecule, barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A target nucleic acid molecule in the present disclosure may comprise a CRISPR guide nucleic acid molecule or other molecule used with gene editing. Processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent binding regions of a nucleic acid molecule, linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.