The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

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.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

The subject invention pertains to methods for the analysis of pooled samples without the need of retesting through the use of oligonucleotide hybridization and target-specific amplification reactions. Specifically, a series of identifier oligonucleotides with different sequence compositions, each corresponding to a distinct sample, are combined into the target template of interest through nucleic acid synthesis. The aforementioned products are pooled together, and the pooled samples are amplified and detected using the probe-based hybridization assay or a size separation module to identify if any of the pool of samples test positive, as well as simultaneously identifying which sample is positive for the targeted sequence.

The subject invention pertains to methods for the analysis of pooled samples without the need of retesting through the use of oligonucleotide hybridization and target-specific amplification reactions. Specifically, a series of identifier oligonucleotides with different sequence compositions, each corresponding to a distinct sample, are combined into the target template of interest through nucleic acid synthesis. The aforementioned products are pooled together, and the pooled samples are amplified and detected using the probe-based hybridization assay or a size separation module to identify if any of the pool of samples test positive, as well as simultaneously identifying which sample is positive for the targeted sequence.

Disclosed herein are methods and systems for classifying cell labels, for example identifying a signal cell label. In some embodiments, the method comprises: obtaining sequencing data of barcoded targets created using targets in cells barcoded using barcodes, wherein a barcode comprises a cell label and a molecular label. After ranking the cell labels, a minimum of a second derivative plot of a cumulative sum plot can be determined. Using the methods, a cell label can be classified as a signal cell label or a noise cell label based on the number of molecular labels with distinct sequences associated with the cell label and a cell label threshold.

Disclosed is a method for determining a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons; sequencing each amplicon in the pool of amplicons to obtain sequence information of each amplicon; comparing a part of the sequence information of each amplicon with at least a part of the sequence of the target specific primer section, wherein the part of the sequence information of each amplicon is a sequence starting from position X-y and y is positive integer; determining whether the part of the sequence information of each amplicon comprises at least the part of the sequence of the target specific primer section; and determining accurate sequence of the target region using sequence information which comprises at least the part of the sequence of the target-specific primer section.