Embodiments of the present disclosure present systems, devices and methods for fragmenting high-molecular weight (HMW) genomic DNA (HMW DNA). In some embodiments, a HMW DNA sample is provided, then, one or more reagents are added to the HMW DNA sample to produce a HMW DNA sample mixture. Thereafter, a Cas9 preparation is added to the HMW DNA sample mixture establishing a HMW DNA – Cas9 mixture where it is then incubated, the Cas9 enzyme is inactivated, and the fragmented DNA purified.
Embodiments described herein relate to systems, devices, and methods for performing preparative electrophoresis. In some embodiments, a housing defines a plurality of cavities each configured to receive a vertical channel. Each vertical channel may include a hydrogel defining a sample well configured to receive a sample of DNA fragments. The vertical channel may be placed in fluidic communication with at least a first reservoir and a second reservoir. In some embodiments, preparative electrophoresis may be completed for the plurality of vertical channels simultaneously. The embodiments described herein may be integrated into automatic workflows for high-throughput applications. The embodiments described herein may be used for both long-read and short-read sequencing applications.
G01N 27/30 - Electrodes, e.g. test electrodesHalf-cells
G01N 11/10 - Investigating flow properties of materials, e.g. viscosity or plasticityAnalysing materials by determining flow properties by moving a body within the material
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
C12N 15/11 - DNA or RNA fragmentsModified forms thereof
3.
SYSTEMS, DEVICES, AND METHODS FOR ELECTROPHORETIC EXTRACTING AND ENRICHING EXTRACHROMOSOMAL DNA
Embodiments of the present disclosure present methods, systems, and devices for extrachromosomal DNA extraction, and in some embodiments, isolation of DNA therefrom, and/or analysis of the extracted and/or isolated DNA, including, in some embodiments, ecDNA.
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
Embodiments of the present disclosure present methods, systems, and devices for extrachromosomal DNA extraction, and in some embodiments, isolation of DNA therefrom, and/or analysis of the extracted and/or isolated DNA, including, in some embodiments, ecDNA.
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
An electrophoresis cassette may include sample well(s), gel column(s) containing a separation gel, and elution modules arranged adjacent the gel column(s). A sample may be provided to the electrophoresis cassette and high-molecular weight (HMW) DNA may be isolated from the sample. Single-copy DNA sequences may be cleaved on both sides of a repeat region of the DNA sequences to produce a cleaved sample, which then may be fractionated using gel electrophoresis. DNA fractions may be isolated from consecutive sections of the separation gel and subjected to PCR assays to detect single-copy sequences within the DNA fraction, said single-copy sequence containing repeat expansion sequences. The subjected DNA fractions may be electroeluted into the plurality of elution modules. A size of DNA fractions having the repeat expansion sequences may be determined. It is also determined if that size is above a normal repeat size range.
A cassette for retaining molecules during electrophoresis has a housing with a lane configured therein. The lane has a first elongate edge and a second elongate edge, and an elution module is configured to be received in the late to divide the lane into a first chamber and a second chamber. A first buffer reservoir is positioned adjacent the first elongate edge, and a second buffer reservoir is positioned adjacent the second elongate edge. The first side of the elution module facing the first chamber comprises a porous sterile filtration membrane. The second side of the elution module facing the second chamber comprises an ultrafiltration membrane that has a pore size to retain molecules during electrophoresis.
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
An electrophoresis cassette may include sample well(s), gel column(s) containing a separation gel, and elution modules arranged adjacent the gel column(s). A sample may be provided to the electrophoresis cassette and high-molecular weight DNA may be isolated from the sample. Single-copy DNA sequences may be cleaved on both sides of a repeat region of the DNA sequences to produce a cleaved sample, which then may be fractionated using gel electrophoresis. DNA fractions may be isolated from consecutive sections of the separation gel and subjected to PCR assays to detect single-copy sequences within the DNA fraction, said single-copy sequence containing repeat expansion sequences. The subjected DNA fractions may be electroeluted into the plurality of elution modules. A size of DNA fractions having the repeat expansion sequences may be determined. It is also determined if that size is above a normal repeat size range.
G01N 27/26 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variablesInvestigating or analysing materials by the use of electric, electrochemical, or magnetic means by using electrolysis or electrophoresis
Various implementations disclosed herein relate to automated processing of nucleic acids and electrophoretic sample preparation. An exemplary disposable cassette for automated molecular processing may include a base housing, a central channel arranged in the housing, and an elution module configured to be received in central channel and to divide the central channel into a first chamber and a second chamber. The elution module comprises a housing having a proximal side, a distal side and an elution module channel passing from the proximal side to the distal side. The elution module also comprises a first membrane attached to a proximal side of the elution module, a second membrane attached to a distal side of the elution module, and a porthole in fluid communication with the elution module channel and configured for receiving a sample.
The disclosure provides cassettes, electrophoresis systems, methods for making the device, and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
A nucleic acid sample may be provided, and the sample may be treated by applying a first enzymatic nucleic acid modifying reagent to produce a first nucleic acid solution. A first protease reagent may be applied to the first nucleic acid solution to produce a second nucleic acid solution. The application of the first protease reagent may completely or substantially inactivate the first enzymatic nucleic acid modifying reagent. A first inhibitor reagent may be applied in order to produce a third nucleic acid solution, and the first inhibitor reagent may completely or substantially inactivate the first protease reagent.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12N 9/00 - Enzymes, e.g. ligases (6.)ProenzymesCompositions thereofProcesses for preparing, activating, inhibiting, separating, or purifying enzymes
C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
G01F 11/00 - Apparatus requiring external operation adapted at each repeated and identical operation to measure and separate a predetermined volume of fluid or fluent solid material from a supply or container, without regard to weight, and to deliver it
19.
APPARATUSES, METHODS AND SYSTEMS FOR AUTOMATED PROCESSING OF NUCLEIC ACIDS AND ELECTROPHORETIC SAMPLE PREPARATION
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
In some embodiments, a method for manipulating DNA molecules for use in a microfluidic device is provided, where the method may comprise providing a solution of a plurality of DNA molecules having a first radius of gyration under under a zero flow velocity, and maintaining the DNA molecules in a spherical shape under a flow velocity.
G01N 15/02 - Investigating particle size or size distribution
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
21.
APPARATUSES, METHODS AND SYSTEMS FOR AUTOMATED PROCESSING OF NUCLEIC ACIDS AND ELECTROPHORETIC SAMPLE PREPARATION
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
The disclosure provides cassettes, electrophoresis systems, methods for making the device, and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
The disclosure provides an electrophoresis cassette (502) comprising a macrofluidic separation channel (525) for separating a sample, elution channels (522,523) for extracting the separated fractions from the separation channel and elution modules (524) for collecting the extracted separated fractions. Methods for making the device, and and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
The disclosure provides an electrophoresis cassette (502) comprising a macrofluidic separation channel (525) for separating a sample, elution channels (522,523) for extracting the separated fractions from the separation channel and elution modules (524) for collecting the extracted separated fractions. Methods for making the device, and and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
Systems and methods for processing fluid samples are disclosed. Fluid sample processing is accomplished using a series of microfluidic bump arrays include an automated and integrated system for sorting particles from a biological sample, lysing those particles to expose total RNA or DNA, purifying the RNA or DNA, processing the RNA or DNA by chemical or enzymatic modification, to select RNA or DNA molecules by size, or to generate, optionally, a sequencing library. The sequencing library is suitable for use in next generation sequencing ("NGS").
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
The invention provides an electrophoresis cassette, wherein a macrofluidic separation channel (9) splits into separate portions (5, 6), one of which having an elution chamber (28) being formed by an analyte-permeable barrier (32) and an analyte-impermeable barrier (33).
The invention provides an electrophoresis cassette, wherein a macrofluidic separation channel (9) splits into separate portions (5, 6), one of which having an elution chamber (28) being formed by an analyte-permeable barrier (32) and an analyte-impermeable barrier (33).
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