Abstract: Disclosed herein include systems, methods, compositions, and kits for in situ readout of barcodes, such as DNA barcodes. Barcode constructs containing a promoter (e.g., a phage promoter) that is inactive in live cells can be integrated in the genomes of cells. Cells can be fixed, and phage RNA polymerase can be used for transcription of the barcode to RNA transcripts. The RNA transcripts can be detected using, for example, fluorescent imaging and used to determine barcode sequences.

Abstract: Apparatus and methods to identify nucleotides of a DNA strand. The method includes exposing the DNA strand to a first dye or peptide, attaching the first dye or peptide to a first type of nucleotide (A,T,C,G) of the DNA strand, the first dye or peptide changing a conductance of the first type of nucleotide to which the first dye or peptide is attached, and measuring a tunneling current signal for all nucleotides of the DNA strand, the changed conductance of the first type of nucleotide providing amplified tunneling current discrimination of the nucleotides of the DNA strand.

Abstract: Processes and kits for preparing a plurality of multiplex amplification products for targeted next generation-sequencing providing reduced background noise.

Abstract: The present invention provides a method for detecting a microorganism in a sample, the method comprising: a) filtering a sample through a filter to entrap any microorganisms present in the sample; b) treating the filter to release genomic material or DNA from the entrapped microorganisms; c) amplifying the genomic material or DNA released from the entrapped microorganisms; and d) identifying specific regions of the genomic material or DNA to determine the presence, identify the species or quantify the approximate number of any entrapped microorganisms.

Abstract: The present invention relates to a method for the isolation of a target nucleic acid region. In particular, said method comprises the steps of contacting a population of nucleic acid molecules with at least one Type II Cas protein-gRNA complex, wherein said gRNA comprises a guide segment that is complementary to the sequence comprised in the target region of at least one nucleic acid molecule, thereby forming a Type II Cas protein-gRNA-nucleic acid complex, contacting the population of nucleic acid molecules with at least one enzyme having exonuclease activity, and isolating the target nucleic acid region from the Type II Cas protein-gRNA-nucleic acid complex.

Abstract: A DNA sequencing device having a first conductor electrically insulated from a second conductor, a voltage source and an amplifier electrically connected in series with the first conductor and the second conductor, a DNA polymerase attached to the first conductor and to the second conductor with matching biotinylated tag molecules, and an electric current monitor. A non-discriminating electrical signal is provided by the polymerase during pairing, which signal can be used as a marker to indicate that transcription is occurring between a single-type of free nucleotide and a base nucleotide of a template DNA strand.

Abstract: The present disclosure provides methods, compositions, and systems employing blocked primers. Aspects of the disclosure include providing a blocked primer reaction mixture that includes a blocked primer and a template nucleic acid component from a single cell; unblocking the blocked primer to produce an active primer reaction mixture and subjecting the activated primer reaction mixture to primer extension conditions, such as nucleic acid amplification conditions.

Abstract: Provided herein are methods and systems for the simultaneous targeted detection and sequencing of DNA, RNA, and Protein. In typical embodiments, the DNA, RNA, and Proteins are detected, characterized, and sequenced using just a single mammalian cell. One embodiment of detecting and characterizing DNA, RNA, or protein from a mammalian cell includes encapsulating a single cell in a drop and performing a protease digest on the encapsulated cell drop, performing a reverse transcriptase reaction; performing a droplet merger with barcoding PCR reagents and barcoding beads; performing a PCR reaction to attach the cell barcodes to the DNA targeted amplicons, RNA targeted amplicons, and protein tag amplicons, where all amplicons from the same emulsion contain the same cell barcode; and detecting and characterizing a DNA, RNA, or protein amplicon by sequencing the cell barcode incorporated into each amplicon.

Abstract: A preparation method for in-situ hybridization probes as follows: fragmenting objective DNAs, recovering 150-600 bp fragments, and after an enzyme modification, ligating, at intervals, the fragments with DNA adaptors containing restriction enzyme site sequences to large DNA loops and long chains; obtaining and labeling a large amount of DNAs in step A or B: A. isothermal amplifying, adding a single nucleotide substrate with a marker when amplifying, to obtain a DNA product with a marker; or B. isothermal amplifying, doping a single nucleotide substrate with a marker to the obtained product with a nick translation or random primer method, to obtain a DNA product with a marker; and digesting the DNA product with the marker by using corresponding restriction enzyme, to obtain in-situ hybridization probes with lengths of 150-600 bp. The method of the present invention accurately controls length range of the probes, reduces production cost, and improves product quality.

Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.

Abstract: Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease.

Abstract: The present invention relates to method of detecting and characterizing one or more Borrelia species causing Lyme Disease or tick-borne relapsing fever within a sample from a subject, the method comprising: a) subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting at least one region of Borrelia 16S rRNA and at least one region of flaB, ospA, ospB, ospC, glpQ, 16S-23S intergenic spacer (IGS1), 5S-23S intergenic spacer (IGS2), bbk32, dbpA, dbpB, and/or p66; and b) analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Borrelia species.

Abstract: Methods are provided for nucleic acid analysis wherein a target nucleic acid is mixed with a dsDNA binding dye to form a mixture. Optionally, an unlabeled probe is included in the mixture. A melting curve is generated for the target nucleic acid by measuring fluorescence from the dsDNA binding dye as the mixture is heated. Dyes for use in nucleic acid analysis and methods for making dyes are also provided.

Abstract: A method for amplification in a microfluidic assay, includes binding an analyte to a transport element, wherein the transport element includes a particle and a first antibody element and the analyte is bound to the first antibody element; moving the transport element with the analyte towards a tracer storage site including tracer elements which includes a first binder element, a label element and a second antibody element; binding the analyte to the second antibody element; moving the transport element with the analyte and the tracer element towards a tracer transport site including second binder elements; binding the first binder element with a second binder element; moving the transport element with the analyte towards the tracer storage site so that the analyte is detached from the second antibody element of the tracer element while the first binder element remains bound to the second binder element.

Abstract: The invention relates to methods of detecting a genetic variation in a genetic sample from a subject using labeled probes and counting the number of labels in the probes.

Abstract: Provided herein are compositions, systems, and methods for detecting microorganisms. In particular, provided herein are compositions, systems, and methods for rapid, multiplex detection of microorganism in unpurified biological samples.

Abstract: Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.

Abstract: A microfluidic emulsion droplet generation system and methods of use thereof are provided. The system may include a microfluidic substrate having a flow path configured and arranged for emulsion droplet generation, at least one textured surface in the flow path configured and arranged for inducing surface-mediated coalescence of emulsion droplets; and at least one channel junction in the flow path for emulsion droplet formation.

Abstract: Methods, compositions and kits for capturing, detecting and quantifying mature small RNAs are provided herein. Embodiments of the methods comprise tailing both the 5? and 3? ends of mature small RNA by ligating a 5? ligation adaptor to the 5? end and polyadenylating the 3? end. Other embodiments comprise reverse transcribing the adaptor ligated, polyadenylated mature small RNA with a universal reverse transcription primer and amplifying the cDNA with universal primers.