Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: The present disclosure relates to improved methods for detecting nucleic acids using DNA fingerloop stem loop structures, wherein the DNA fingerloop stem loop structures diminish base pairing of a detection probe to a mismatched target nucleic acid. The present disclosure also relates to improved methods for amplifying nucleic acids. Further disclosed are chimeric fingerloop DNAs for use in methods for modulating protein expression levels and/or RNA stability.

Abstract: The present disclosure provides, inter alia, methods and compositions (e.g., conjugates) for imaging, at high spatial resolution, targets of interest.

Abstract: Disclosed herein are methods and compositions relating to synthesized nanopores. The synthesized nanopores can be used for detecting a target molecule (e.g. RNA, DNA, or peptide).

Abstract: Disclosed herein are compositions and methods for detecting RNA binding sites and RNA interacting partners involving the use of a modified capture oligonucleotide having a dual toehold design.

Abstract: Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.

Abstract: This present disclosure describes hybridization probes modularly constructed from several oligonucleotides with a pattern of designed complementary interactions, allowing the probes to sequence-specifically capture or analyze nucleic acid target sequences that are long and/or complex.

Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.

Abstract: There are provided methods and systems for detecting and/or quantifying an analyte. In particular, there are provided methods and systems for simultaneous detection and/or quantitation of two or more analytes in a sample. In some embodiments, there are provided colocalization-by-linkage assays on microparticles (CLAMP) comprising two sets of binders pre-assembled on a support, such that the two sets of binders are colocalized before contacting the sample.

Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.

Abstract: Provided herein, in some embodiments, are methods and compositions for highly multiplexed in situ signal amplification via hairpin-mediated concatemerization.

Abstract: The present invention provides a method for improving the loading of nucleic acid on a solid support by contacting the solid support with a poloxamer-containing reagent. The present invention also provides a method for improving the stability of a nucleic acid on a solid support, comprising contacting a nucleic acid molecule with a partially double-strand oligonucleotide before or after loading the nucleic acid molecule on a solid support, so as to cause the nucleic acid molecule to hybridize with the oligonucleotide. The present invention also provides a combined use of the two methods.

Abstract: The present disclosure provides methods, devices and systems for detecting a presence of a nucleic acid molecule having a nucleic acid sequence. Detection of cyclic single base extension can be used to detect a nucleic acid molecule hybridized to a probe and detect a presence of a nucleic acid. The methods disclosed herein can detect a nucleic acid molecule present in a nucleic acid sample at low concentrations and in the presence of background nucleic acids having high sequence similarity.

Abstract: A membrane-spanning nanopore is provided that comprises: i. at least one scaffold polynucleotide strand; ii. a plurality of staple polynucleotide strands; and iii. at least one hydrophobically-modified polynucleotide strand, wherein the at least one hydrophobically-modified polynucleotide strand comprises a polynucleotide strand and a hydrophobic moiety; wherein each of the plurality of staple polynucleotide strands hybridises to the at least one scaffold polynucleotide strand to form the three-dimensional structure of the membrane-spanning nanopore, and wherein the at least one hydrophobically-modified polynucleotide strand hybridises to a portion of the at least one scaffold polynucleotide strand, the membrane-spanning nanopore defining a central channel with a minimum internal width of at least about 5 nm. Membranes comprising the membrane-spanning nanopore and applications of those membranes are also provided.

Abstract: The invention relates to imaging, such as in situ imaging by expansion microscopy, labelling, and analyzing biological samples, such as formalin fixed paraffin embedded (FFPE) cells and tissues, as well as reagents and kits for doing so.

Abstract: The present invention relates to a method for reducing intracellular non-specific staining caused by a metal complex, and a method for improving specific staining. When a cell is stained by the method of the present invention, intracellular non-specific staining, which inevitably occurs when a metal complex is used, can be minimized, and as a result, specific staining for a target organelle can be effectively induced.

Abstract: Provided herein are materials and methods for isolation of eukaryotic nucleic acid from a human or non-human animal stool sample. Also provided are methods of analysis of eukaryotic biomarkers present in a human or non-human animal stool sample.