Abstract: The present disclosure generally relates to methods and compositions for interrogating and/or analyzing DNA methylation in a biological sample. In some aspects, the present disclosure relates to methods for determining the methylation status of a region of interest of genomic DNA. In some aspects, the methylation status is analyzed by interrogating converted DNA in which the sequence of the converted DNA is indicative of the methylation state of the DNA. In some aspects, the methods comprise generating a collective signal that is based on the methylation states of a plurality of sequences or residues in the DNA, and that is representative of the methylation status of the region of interest as a whole.

Abstract: The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising generating a rolling circle amplification product (RCP) using a target ribonucleic acid (RNA) as a primer. In some aspects, RNase H and a nucleic acid oligonucleotide are used to generate a free 3? end of the target RNA to prime RCA.

Abstract: The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising generating a rolling circle amplification product (RCP) using a target ribonucleic acid (RNA) as a primer. In some aspects, RNase H and a nucleic acid oligonucleotide are used to generate a free 3? end of the target RNA to prime RCA.

Abstract: The present disclosure relates in some aspects to methods for analyzing a target nucleic acid in a biological sample (e.g., cell or tissue sample). In some aspects, provided herein are methods and compositions for analyzing a target nucleic acid in a ligation-based assay using one or more probes, and phosphorylation of one or more probes hybridized to a target nucleic acid is performed.

Abstract: The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising generating a rolling circle amplification product (RCP) using a target ribonucleic acid (RNA) as a primer. In some aspects, RNase H and a nucleic acid oligonucleotide are used to generate a free 3? end of the target RNA to prime RCA.

Abstract: The present disclosure relates in some aspects to compositions and methods of using Phi29 polymerase fusion proteins. In some aspects, the compositions and methods provided herein address certain limitations associated with the Phi29 polymerase. In some aspects, the composition and methods disclosed herein provide more robust nucleic acid amplification for improved in vitro and in situ analysis.

Abstract: Devices and methods useful for sequencing and characterizing single nucleic acid molecules involve large arrays of nanopore zero-mode waveguides (NZMWs). The methods and devices are made possible by fabrication of nanoporous membranes of appropriate porosity for use in nucleotide sequencing. The fabrication methods eliminate the need for serial nanopore formation and make possible the mass production of highly efficient DNA and RNA single molecule sequencing devices.

Abstract: Described herein are systems for analysis of biopolymers and complexes containing biopolymers based on optical measurement of ion flux through pores. Also described are methods of using such devices for analysis of biopolymers and complexes containing biopolymers, including methods of determining the nucleotide sequences of polynucleotides.

Abstract: Devices and methods useful for sequencing and characterizing single nucleic acid molecules involve large arrays of nanopore zero-mode waveguides (NZMWs). The methods and devices are made possible by fabrication of nanoporous membranes of appropriate porosity for use in nucleotide sequencing. The fabrication methods eliminate the need for serial nanopore formation and make possible the mass production of highly efficient DNA and RNA single molecule sequencing devices.

Abstract: Described herein are systems for analysis of biopolymers and complexes containing biopolymers based on optical measurement of ion flux through pores. Also described are methods of using such devices for analysis of biopolymers and complexes containing biopolymers, including methods of determining the nucleotide sequences of polynucleotides.