The invention relates to methods for purifying and isolating at least one RNA molecule which interacts with an RNA-binding protein (RBP). The invention also provides nucleic acid adaptors and primers for use in such methods.

The invention relates to methods for purifying and isolating at least one RNA molecule which interacts with an RNA-binding protein (RBP). The invention also provides nucleic acid adaptors and primers for use in such methods.

Described herein are affinity-labeled polypeptide compositions, such as affinity-labeled transcription factor compositions, and methods of using such compositions to evaluate interactions of the polypeptide with other molecules such as nucleic acids.

Described herein are affinity-labeled polypeptide compositions, such as affinity-labeled transcription factor compositions, and methods of using such compositions to evaluate interactions of the polypeptide with other molecules such as nucleic acids.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein allow for detection of a target sequence by rolling circle amplification without requiring a ligation step and without sacrificing specificity (e.g., rolling circle amplification occurs only for circular probes and/or hairpin molecules specifically hybridized to a target sequence).

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein allow for detection of a target sequence by rolling circle amplification without requiring a ligation step and without sacrificing specificity (e.g., rolling circle amplification occurs only for circular probes and/or hairpin molecules specifically hybridized to a target sequence).

A method for detecting a target nucleic acid fragment in a sample, the method including a step of bringing the sample into contact with a gRNA, a Cas protein, and a substrate nucleic acid fragment, in which the Cas protein expresses nuclease activity after forming a complex with the gRNA and the target nucleic acid fragment, the substrate nucleic acid fragment is labeled with a fluorescent substance and a quenching substance, when the substrate nucleic acid fragment is cleaved by the nuclease activity so that the fluorescent substance is separated from the quenching substance, the fluorescent substance emits fluorescence due to excitation light, and the contact is performed in a reaction space having a volume of 10 aL to 100 pL so that when the target nucleic acid fragment is present in the sample, a tripartite complex is formed, the substrate nucleic acid fragment is cleaved, and the fluorescent substance is separated from the quenching substance; and a step of irradiating the fluorescent substance with the excitation light and detecting the fluorescence, in which detection of the fluorescence indicates that the target nucleic acid fragment is present in the sample.

A method for detecting a target nucleic acid fragment in a sample, the method including a step of bringing the sample into contact with a gRNA, a Cas protein, and a substrate nucleic acid fragment, in which the Cas protein expresses nuclease activity after forming a complex with the gRNA and the target nucleic acid fragment, the substrate nucleic acid fragment is labeled with a fluorescent substance and a quenching substance, when the substrate nucleic acid fragment is cleaved by the nuclease activity so that the fluorescent substance is separated from the quenching substance, the fluorescent substance emits fluorescence due to excitation light, and the contact is performed in a reaction space having a volume of 10 aL to 100 pL so that when the target nucleic acid fragment is present in the sample, a tripartite complex is formed, the substrate nucleic acid fragment is cleaved, and the fluorescent substance is separated from the quenching substance; and a step of irradiating the fluorescent substance with the excitation light and detecting the fluorescence, in which detection of the fluorescence indicates that the target nucleic acid fragment is present in the sample.

A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.