Abstract: The present disclosure relates to systems and methods of analyzing cleavage profiles of nucleases.

Abstract: In some aspects disclosed herein are methods and compositions for detecting a target nucleic acid molecule, said method comprising performing a linear oligo hybridization chain reaction (LO-HCR) to generate a polymeric product, and detecting the polymeric product, thereby detecting the target nucleic acid molecule.

Abstract: The present invention relates to a mutant reverse transcriptase (RT) with increased thermal stability relative to the wildtype, a nucleic acid encoding the mutant RT, a cell comprising the mutant RT or the nucleic acid, a kit comprising the mutant RT, the use of the mutant RT for cDNA synthesis, method for reverse transcription of RNA comprising synthesizing cDNA with the use of the mutant RT and a method for detecting an RNA marker in a sample with the use of the mutant RT.

Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.

Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

Abstract: Presented are methods and compositions for obtaining sequence information from one or more individual cells. The methods are useful for obtaining sequence information for a single nucleotide sequence, and for multiplex generation of sequence information from one or more individual cells.

Abstract: Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.

Abstract: Disclosed herein, inter alia, are compositions and methods for efficient amplification and sequencing of nucleic acid templates.

Abstract: The present application provides compositions, systems, and methods for encoding and decoding nucleic acid molecules.

Abstract: The merocyanine compound of the present invention causes a spectral change of a hypochromic shift in the vicinity of the wavelength of 512 nm by intercalation between dsRNA nucleotide pairs, and the spectral change shows high accuracy and reproducibility, so the merocyanine compound of the present invention can be effectively used for detecting dsRNA and comparing the expression levels between samples. In addition, the present invention relates to a composition for detecting dsRNA comprising a merocyanine compound, a salt thereof or an isomer thereof.

Abstract: The present disclosure provides, in some embodiments, methods and compositions for single-molecule detection.

Abstract: A method comprises (a) providing single-stranded DNA; (b) ligating a first adapter to a 3? end of the single-stranded DNA to form a once adapter ligated nucleic acid strand, the first adapter having a first protruding random sequence that is at least 3 bases long and that acts as a splint to join the single-stranded DNA with the first adapter; (c) ligating a second adapter to a 5? end of the once adapter ligated nucleic acid strand to form a twice ligated nucleic acid strand, the second adapter having a second protruding random sequence that is at least 3 bases long and that acts as a splint to join the once adapter ligated nucleic acid strand with the second adapter; and (d) performing an amplification reaction on the twice ligated nucleic acid strand, thereby generating copies of the twice ligated nucleic acid strand.

Abstract: Disclosed herein are methods for performing in situ sequencing of RNA transcripts with non-uniform 5? ends. During reverse transcription (RT) of RNA transcripts, RT enzyme is induced to “template-switch” to a separate oligonucleotide provided as the template for the upstream flanking region. This flanking region is grafted onto the beginning of the cDNA, enabling padlock probe detection, rolling circle amplification, and fluorescent in situ sequencing. Overall, the disclosed method for in situ sequencing can be applicable for analyzing exogenously introduced transcripts (e.g., identifying and determining impact of a perturbation including a CRISPR perturbation or shRNA/siRNA/ASO perturbation), analyzing naturally occurring transcripts (e.g., measuring gene expression, detecting splicing events), and analyzing modified, naturally occurring transcripts (e.g., detecting mutations or gene edits).

Abstract: In some aspects, the present disclosure provides methods for forming ligation products comprising single-stranded polynucleotides. Ligation products formed by various aspects of the present disclosure can be useful for various applications, including but not limited to sequence analysis. In some embodiments, the ligation products comprise cell-free polynucleotides. In some aspects, the present disclosure provides reaction mixtures, kits and complexes consistent with the methods herein.

Abstract: Disclosed is a DNA sequencing method. The DNA sequencing method of this invention comprises: (1) adding a tag sequence at the 3? terminus of the DNA to be sequenced so as to form a DNA to be sequenced including the tag sequence, the nucleotide sequence of said tag sequence being the reverse complement of the nucleotide sequence of the sequencing primer; (2) mixing the DNA to be sequenced including the tag sequence and the sequencing primer so as to form a product having a 5? terminus double strand and a single main strand; (3) after step (2) is completed, the product is mixed separately with dATP, dCTP, dTTP, and dGTP to obtain four systems, each system is separately added to a single-molecule device modified by a DNA polymerase, and electric signals are read. Experiments verify that the method of this invention performs DNA sequencing and has important application value.

Abstract: Presented herein are methods and compositions for concatenating template strands during the bridge amplification process. The methods are useful for surface amplification at improved densities. The methods and compositions provided herein enable creation of clusters that are brighter, but at the same densities as currently achieved using standard cluster amplification.

Abstract: The present disclosure discloses a detection kit for Salmonella typhi, a preparation method and an application thereof, the detection kit includes: amplification primer, crRNA, LbCas12a-RR protein and a single-stranded DNA reporting system, the crRNA is a specific crRNA for a detection segment of the flag gene of Salmonella typhi; a LbCas12a-RR protein expression sequence is a prokaryotic codon optimized with a Cas12 protein nucleic acid sequence, and amino acid positions of 532 and 595 are mutated into G532R and K595R, respectively. The application of the kit is, to use the detection kit of Salmonella typhi for nucleic acid detection of Salmonella typhi; and the kit has high sensitivity, high specificity and fast visualization.

Abstract: The present disclosure encompasses embodiments of nucleic acids comprising genetic elements which are useful for the detection of diseased cells.

Abstract: The present invention relates to a genetic probe comprising: a nanoparticle; an oligonucleotide probe anchored to the surface of the nanoparticle, comprising an oligonucleotide backbone with a tag incorporated therein via a linker group; and a reference probe anchored to the surface of the nanoparticle, wherein the reference probe comprises a marker; wherein either (a) the tag is an organic fluorescent tag and the marker is a transition metal-based fluorescent marker; or (b) the tag is a redox-active tag and the marker is a transition metal-based redox-active marker. The invention also relates to a composition or kit containing a probe of the invention.

Abstract: Methods for purifying RNA from a sample, comprising one or more steps of tangential flow filtration, hydroxyapatite chromatography, core bead flow-through chromatography, or any combinations thereof. These techniques are useful individually, but show very high efficiency when used in combination, or when performed in particular orders. The methods can purify RNA in a highly efficient manner without unduly compromising potency or stability, to provide compositions in which RNA is substantially cleared of contaminants. Moreover, they can be performed without the need for organic solvents.