Abstract: Methods for rapidly and accurately detecting genetic material from hop latent viroid RNA (HLVd) that combines reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology with specific oligonucleotide primers, fluorophore-labeled oligonucleotide primers, quencher-conjugated oligonucleotide primers, pH buffers, and enzymes, are described. The methods include at least one internal positive control targeting sequence, for minimizing false positive and false negative results, thereby allowing more certain interpretation of the results. The reaction can be performed at a single elevated temperature, can be completed in 1-1.5 hours, and the results can readily be interpreted by visually observing the fluorescence color of the reaction using ultraviolet light, or by using an electronic image acquisition system for viewing fluorescence results from one or more reactions.

Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

Abstract: Disclosed herein, inter alia, are compositions and methods for efficient transfer and analyses of cellular material, tissue samples, such as tissue sections, using carrier substrates.

Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids fragmented with a transposase enzyme in a biological sample.

Abstract: Systems and methods for tissue classification are provided. An image of tissue on a substrate is obtained as a plurality of pixels. Fiducial markers are on the substrate boundary. Pixels are assigned to a first class, indicating tissue sample, or a second class, indicating background. The assigning uses the fiducial markers to define a bounding box within the image and disregards pixels outside the box. Then, heuristic classifiers are applied to the pixels: for each respective pixel in the plurality of pixels, each heuristic classifier votes for the respective pixel between the first and second class, thereby forming an aggregated score for each pixel that in one of first class, likely first class, likely second class, and obvious second class. The aggregated score and intensity of each pixel is applied to a segmentation algorithm to assign a probability to each pixel of being tissue sample or background.

Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.

Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.

Abstract: Disclosed herein, interalia, are compounds, compositions, and methods of using the same for the sequencing of a nucleic acid.

Abstract: Microfluidic channels networks and systems are provided. One network includes a first fluid channel having a first depth dimension; at least a second channel intersecting the first channel at a first intersection; at least a third channel in fluid communication with the first intersection, at least one of the first intersection and the third channel having a depth dimension that is greater than the first depth dimension. Also provided is a flow control system for directing fluids in the network. Systems are additionally provided for flowing disrupted particles into a droplet formation junction, whereby a portion of the disrupted particles or the contents thereof are encapsulated into one or more droplets. Further provided is a method for controlling filling of a microfluidic network by controlling passive valving microfluidic channel network features.

Abstract: Disclosed herein, inter alia, are methods of detecting or sequencing circular template polynucleotides on a solid support and/or in cells and tissues.

Abstract: Provided herein are methods of making, amplifying, and sequencing tagged nucleic acid complements, compositions including interposing oligonucleotide barcodes, and kits useful in obtaining long-range sequence data.

Abstract: The disclosure provides recombinant reverse transcriptases comprising one or more DNA binding domains conjugated to an engineered reversed transcriptase that have been modified to exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both. The disclosure further provides compositions and kits comprising the recombinant reverse transcriptase enzymes and methods of producing, amplifying or sequencing nucleic acid molecules using these fusion reverse transcriptase enzymes.

Abstract: Methylation biomarker selection apparatuses and methods are provided. A methylation biomarker selection apparatus stores a plurality of first data sets and a plurality of second data sets, wherein each of the first data sets includes a plurality of methylation degrees corresponding to a plurality of methylation loci, and each of the second data sets includes at least one medical record. The methylation biomarker selection apparatus determines a plurality of primary biomarkers by identifying a plurality of differentiable loci from the methylation loci according to the methylation degrees, determines a plurality of secondary biomarkers by identifying a plurality of comorbidities of a target disease, and associated genes thereof based on the second data sets, and determines a plurality of candidate biomarkers based on a correlation analysis of the primary biomarkers and the secondary biomarkers.

Abstract: The present disclosure pertains to techniques that leverage machine learning models to identify tumor-specific mutations through an integrated analysis of next generation sequencing data. In a particular aspect, a computer-implemented method is provided that includes generating sequence reads from one or more samples collected from the same patient, generating variant call files by analyzing the sequence reads corresponding respectively to the one or more samples, comparing variant call files to generate a list of candidate somatic variants, generating, by a classification machine learning model, scores for each of the candidate somatic variants in the list of candidate somatic variants, where the scores are generated based on a plurality of classifications generated by the classification machine learning model, determining, based on the scores, a ctDNA status for the patient, where the ctDNA status is either positive or negative, and generating a report that provides the ctDNA status for the patient.

Abstract: Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate.

Abstract: Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.