Abstract: A system may include a horizontal actuator to move a tray, to which a microwell plate and a microfluidic chip may be coupled. The system may include a vertical actuator to move a support arm, to which a plurality of pipettes or pipette tips may be coupled. The system may include a rotational actuator to move an angle bracket, to which a magnet may be coupled. The system may include a heater, through which the pipettes may extend. The system may include a pump to control the flow of fluids through the pipettes. Disclosed methods include performing PCR within the described system.

Abstract: Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from the sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from the sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: Provided herein are methods of improving sensitivity of spatial detection of an analyte in a biological sample using splint oligonucleotides, circularized second strands, and rolling circle amplification. For example, provided herein are methods of improving sensitivity of spatial detection of an analyte in a biological sample where a splint oligonucleotide hybridizes to a second strand; the second strand is ligated together thereby creating a circularized second strand, rolling circle amplification of the circularized second strand results in generation of an amplified second strand, and all or part of the sequence of the amplified second strand is determined and used to spatially detect the analyte in the biological sample.

Abstract: The invention concerns a method for detecting isothermal loop-mediated (LAMP) amplification of a target nucleic acid sequence which is based on the fluorescence resonance energy transfer (FRET) mechanism. The invention also concerns a set of oligonucleotides and a kit adapted for carrying out the LAMP-FRET method of the invention.

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.

Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.

Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.

Abstract: The inventive subject matter includes an antimicrobial peptide vectored composition made of a bacterial protein expression vehicle expressing one or more recombinant antimicrobial peptide effector molecules. More specifically these novel recombinant antimicrobial peptide effector molecules exhibit preferential anti-microbial activity. The utility of the current inventive subject matter has demonstrated a reduced viability of Eimeira acervulina sporozoites in vitro using a sporozoite killing assay. More specifically, the antimicrobial peptide vectored composition is a bacterial protein expression vehicle expressing one or more recombinant antimicrobial peptide effector molecules, wherein the one or more recombinant antimicrobial peptide effector molecules are engineered from a NK-lysin gene and the one or more recombinant antimicrobial peptide effector molecules are engineered to express functionally active NK-2.

Abstract: The present invention provides modified oligonucleotides and methods for their use in the detection of nucleic acids. The oligonucleotides and methods find particular application in amplifying and/or detecting areas of genetic variation in target nucleic acid sequences.

Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.

Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.

Abstract: A receptacle cap includes a probe recess configured to receive a probe inserted therein to thereby frictionally secure the receptacle cap to the probe, and a closed lower end of the receptacle is insertable into an open end of a reaction receptacle to close the reaction receptacle. The receptacle cap and the reaction receptacle include interlocking features for securing the receptacle cap to the reaction receptacle.

Abstract: The present invention generally relates to imaging cells, for example, to determine phenotypes and/or genotypes in populations of cells. The cells may be exposed to a nucleic acid comprising an identification portion, which may be used to distinguish the cells from each other. In some embodiments, the cells may be exposed to a nucleic acid comprising an expression portion. The identification portion, the expression portion, or both may be introduced into the genome of a host organism or as exogenous materials, e.g. plasmids.

Abstract: The present disclosure is directed to compositions, methods and kits for amplifying target nucleic acids while reducing non-specific amplification and undesired amplification products using a dual hot start reaction mixture that comprise at least two different hot start mechanisms.

Abstract: A method for capturing ancient DNA of a wooden cultural relic, sequentially includes the following steps: sampling, removing exogenous DNA contamination on the inner part and the outer surface of a sample, and effectively obtaining the ancient DNA of the wooden cultural relic through vacuum freeze-drying dehydration, sample grinding, rinsing, cell lysis, DNA genome enrichment and hybridization and capturing. The method focuses on precise capture of the ancient DNA of the wood cells of the wood cultural relic, not only breaks through the problem that effective acquisition of the DNA of the wood cultural relic is difficult to realize by a conventional wood DNA extraction method, but also provides possibility for analysis and utilization of the ancient DNA with typical characteristics of serious exogenous contamination, low DNA content, high degradation, extensive damage and the like.

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

Abstract: Techniques for positional delivery and position encoding by oligonucleotides of biological cells for single cell RNA sequencing are provided. In one aspect, a method of positional delivery and encoding of cells in a biological sample includes: encoding the cells in the biological sample for single cell sequencing by delivering molecular probes inside the cells that encode a position of the cells in the biological sample. A system for positional delivery and encoding of cells in a biological sample is also provided.

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

Abstract: Methods for making and using reagents and adapters for use in nucleic acid sequencing applications are disclosed herein. In several embodiments, adapters and reagents and the methods of making such adapters and reagents can be used for Duplex Sequencing applications.