Systems and methods for assessing mRNA in vivo and/or in vitro stability are disclosed. Some embodiments methods obtain RNA indexed or barcoded RNA molecules which are then tested against various conditions including stability inside of cells, stability in cell lysate, and stability in solution (e.g., for storage and/or transportation). Additional embodiments describe methods to determine degradation points with single base resolution.

Described herein are methods and systems for performing chemical or enzymatic reactions using electrophoresis. Devices, systems, and methods for preparing a library of tagged nucleic acid fragments from a target double-stranded nucleic acid using electrophoresis are also provided. Application of one or more electric fields causes molecules to migrate through the electrophoresis gel matrix.

Described herein are methods and systems for performing chemical or enzymatic reactions using electrophoresis. Devices, systems, and methods for preparing a library of tagged nucleic acid fragments from a target double-stranded nucleic acid using electrophoresis are also provided. Application of one or more electric fields causes molecules to migrate through the electrophoresis gel matrix.

Provided herein are products and methods for detecting analytes using polymers that bind to such analytes and thereby undergo a conformational change or contribute to a newly formed complex.

Provided herein are products and methods for detecting analytes using polymers that bind to such analytes and thereby undergo a conformational change or contribute to a newly formed complex.

Provided herein are microfluidic devices that can be configured to generate an electrophoretic flow that is in opposition to a fluid flow through a microcapillary of a microfluidic device provided herein. Also provided herein are methods that include adding an amount of particle to the inlet area of a microfluidic device as provided herein, generating a first fluid flow through a microcapillary of a microfluidic device provided herein; and applying a uniform electric field to the microfluidic device, where the uniform electric field generates an electrophoretic flow that is in opposition to the fluid flow.

Provided herein are microfluidic devices that can be configured to generate an electrophoretic flow that is in opposition to a fluid flow through a microcapillary of a microfluidic device provided herein. Also provided herein are methods that include adding an amount of particle to the inlet area of a microfluidic device as provided herein, generating a first fluid flow through a microcapillary of a microfluidic device provided herein; and applying a uniform electric field to the microfluidic device, where the uniform electric field generates an electrophoretic flow that is in opposition to the fluid flow.

Various embodiments are described herein related to an assay, method and apparatus for performing an RNA Disruption Assay (RDA) for cellular RNA optionally in response to a cytotoxic treatment such as chemotherapy and/or radiation treatment. The method comprises obtaining at least one electropherogram dataset corresponding to a unique biological sample comprising the cellular RNA at a time point, optionally during or after the treatment; determining values for features from at least two shifted regions of the at least one electropherogram dataset, the shifting being due to the treatment; and optionally determining an RDA score based on a combination of the values of the features.

Various embodiments are described herein related to an assay, method and apparatus for performing an RNA Disruption Assay (RDA) for cellular RNA optionally in response to a cytotoxic treatment such as chemotherapy and/or radiation treatment. The method comprises obtaining at least one electropherogram dataset corresponding to a unique biological sample comprising the cellular RNA at a time point, optionally during or after the treatment; determining values for features from at least two shifted regions of the at least one electropherogram dataset, the shifting being due to the treatment; and optionally determining an RDA score based on a combination of the values of the features.

The present disclosure relates to compositions and methods of RNA analysis. In particular, the present disclosure provides a method of RNA analysis that includes obtaining a sample, applying one or more multi-partite probes to the sample, where each of the one or more multi-partite probes includes at least two sub-probes, annealing at least one of the applied one or more multi-partite probes to at least one target nucleic acid within the sample, and ligating the at least two sub-probes associated with the at least one annealed multi-partite probe to create a target nucleic acid proxy that can be detected.