WO2023004068A2 - Procédés, dispositifs et kits pour la purification et la lyse de particules biologiques - Google Patents

Procédés, dispositifs et kits pour la purification et la lyse de particules biologiques Download PDF

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Publication number
WO2023004068A2
WO2023004068A2 PCT/US2022/037918 US2022037918W WO2023004068A2 WO 2023004068 A2 WO2023004068 A2 WO 2023004068A2 US 2022037918 W US2022037918 W US 2022037918W WO 2023004068 A2 WO2023004068 A2 WO 2023004068A2
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WO
WIPO (PCT)
Prior art keywords
vessel
kit
flow path
biological particles
outlet
Prior art date
Application number
PCT/US2022/037918
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English (en)
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WO2023004068A3 (fr
Inventor
Stephane Claude BOUTET
Alireza SALMANZADEH
Michael Gibbons
Original Assignee
10X Genomics, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US17/551,761 external-priority patent/US20220348901A1/en
Application filed by 10X Genomics, Inc. filed Critical 10X Genomics, Inc.
Publication of WO2023004068A2 publication Critical patent/WO2023004068A2/fr
Publication of WO2023004068A3 publication Critical patent/WO2023004068A3/fr

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Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5021—Test tubes specially adapted for centrifugation purposes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/50273—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by the means or forces applied to move the fluids
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502753—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
    • B01L2200/0668—Trapping microscopic beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/06—Auxiliary integrated devices, integrated components
    • B01L2300/0681—Filter
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0848—Specific forms of parts of containers
    • B01L2300/0854—Double walls
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0403—Moving fluids with specific forces or mechanical means specific forces
    • B01L2400/0409—Moving fluids with specific forces or mechanical means specific forces centrifugal forces
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/08—Regulating or influencing the flow resistance
    • B01L2400/084—Passive control of flow resistance
    • B01L2400/086—Passive control of flow resistance using baffles or other fixed flow obstructions

Definitions

  • biomedical applications rely on high-throughput assays of samples combined with one or more reagents in droplets or particles.
  • high-throughput genetic tests using target-specific reagents are able to provide information about samples in drug discovery, biomarker discovery, and clinical diagnostics, among others.
  • Many of these applications rely on the presence of a biological particle (e.g., a cell or particulate component thereof, e.g., a nucleus).
  • a biological particle e.g., a cell or particulate component thereof, e.g., a nucleus
  • precise sample preparation may be required before droplet formation.
  • Prior devices and methods for purifying biological particles may disturb and alter its characteristics (e.g., gene expression, activation, or viability). Accordingly, devices and methods for gently and reliably lysing and purifying biological particles would be beneficial.
  • the invention features a method of purifying a biological particle.
  • the method includes providing a vessel that includes an inlet; a first layer including a first liquid having a first density; and a thixotropic layer disposed above the first layer.
  • the method further includes providing a liquid mixture that includes the biological particle to the inlet of the vessel, wherein the density of the liquid mixture is less than the first density; and centrifuging the vessel.
  • the thixotropic layer separates the first layer and the liquid mixture and allows passage of the biological particle to the first layer during centrifugation.
  • the method further includes removing a supernatant liquid after centrifugation.
  • the vessel is inserted in an outer vessel.
  • the vessel includes an outlet.
  • the method further includes opening a tip of the vessel to create the outlet.
  • the method further includes centrifuging the vessel, wherein the biological particle exits the vessel via the outlet and is collected in the outer vessel.
  • the first layer and/or the liquid mixture includes iodixanol.
  • the first layer includes about 30% iodixanol.
  • the liquid mixture includes about 25% iodixanol.
  • the thixotropic layer includes a polymeric gel.
  • the polymeric gel includes polyester.
  • the biological particle is a cell or a particulate component thereof.
  • the biological particle is an organelle, e.g., a nucleus.
  • the invention features a device that includes a centrifuge tube containing a liquid having a predetermined density that is composed of tissue culture medium.
  • the device may contain a liquid having tissue culture medium and a concentration of from about 10% to about 50% iodixanol (e.g., from about 15% to about 45%, from about 20% to about 35%, from about 22% to about 32%, or from about 24% to about 30%).
  • the centrifuge tube may be, for example, a microcentrifuge tube or a PCR tube, or any other suitable structure configured to fit within a centrifuge.
  • the density of the liquid is from about 1.11 g/mL to about 1.12 g/mL (e.g., from about 1.146 g/mL to about 1.175, e.g., about 1.1107 g/mL, 1.117 g/mL, 1.127 g/mL, 1.136 g/mL, 1.146 g/mL, 1.156 g/mL, 1.165 g/mL, or 1.175 g/mL).
  • the liquid may contain iodixanol or a comparable component to create a similar density as iodixanol, such as ficoll, histopaque, or sucrose.
  • the invention features a method of purifying a biological particle by providing a device that includes the centrifuge tube.
  • the method further includes providing a liquid mixture that includes the biological particle to the centrifuge tube and centrifuging the centrifuge tube. During centrifugation, the biological particle moves to the bottom of the centrifuge tube.
  • a first centrifugation step is performed in which all contents of the tissue culture medium are pelleted. Following the first centrifugation, the supernatant may be removed, e.g., via decanting or discarding. A cell culture medium may then be added to the pellet. When this sample is centrifuged, only certain (e.g., desired) biological particles (e.g., cells or particulate components thereof, e.g., nuclei) are pelleted.
  • biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • the invention features a kit that includes an outer vessel and a removable insert configured to fit in the vessel.
  • the removable insert includes an inlet; a first layer including a first liquid having a first density; and a thixotropic layer disposed above the first layer.
  • the thixotropic layer is configured to separate the first layer and a diluent having a density lower than the first density provided to the inlet of the insert.
  • the removable insert includes an outlet.
  • the outlet may include a breakable or removable tip.
  • the first layer includes iodixanol.
  • the first layer includes about 30% iodixanol.
  • the kit further includes the diluent.
  • the diluent may include about 25% iodixanol.
  • the thixotropic layer includes a polymeric gel.
  • the polymeric gel may include polyester.
  • the kit further includes a cell lysis buffer.
  • the cell lysis buffer may include an RNAse inhibitor.
  • the cell lysis buffer may include a surfactant (e.g., from about 0.01% to about 1.0% of the surfactant).
  • the cell lysis buffer includes 10 mM Tris-HCI (pH 7.4), 10 mM NaCI, 3 mM MgCL, 0.01% IGEPAL CA-630 (octylphenoxypolyethoxyethanol), 0.2 U/mI RNase Inhibitor (e.g., enzymatic RNAse inhibitor, e.g., Protector RNAse), 0.1% BSA, 2 mM spermine, and from about 0.01% to about 1.0% of a surfactant/detergent (e.g., TWEEN-20 (polysorbate 20) or IGEPAL CA-630 (octylphenoxypolyethoxyethanol).
  • a surfactant/detergent e.g.,
  • the cell lysis buffer may include 10 mM Tris-HCI (pH 7.4), 10 mM NaCI, 3 mM MgCL, 0.01% IGEPAL CA-630 (octylphenoxypolyethoxyethanol), 0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2 mM spermine, and 0.1% TWEEN-20 (polysorbate 20).
  • the lysis buffer comprises a lysis agent, a reducing agent, and a surfactant.
  • the kit further includes an isotonic buffer.
  • the isotonic buffer may include an RNAse inhibitor.
  • the isotonic buffer may include a surfactant (e.g., from about 0.01% to about 1.0% of the surfactant).
  • the isotonic buffer may include 20 mM Tris-HCI (pH 7.4), 0.25 M sucrose, 25 mM KCI, 5 mM MgCl2, 0.01% IGEPAL CA-630,0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2mM spermine, and 0.1% TWEEN-20 (polysorbate 20).
  • one or more of the buffers described herein are isotonic.
  • one or more of the buffers described herein are not isotonic. In some aspects, one or more of the buffers described herein are not hypertonic. In some aspects, one or more of the buffers described herein are not hypotonic. In some aspects, the lysis buffer described herein is an isotonic buffer. In some aspects, the lysis buffer described herein is not a hypertonic buffer. In some aspects, the lysis buffer described herein is not a hypotonic buffer. In some aspects, the debris removal buffer described herein is an isotonic buffer. In some aspects, the debris removal buffer described herein is not a hypertonic buffer. In some aspects, the debris removal buffer described herein is not a hypotonic buffer. In some aspects, the wash and suspension buffer described herein is an isotonic buffer. In some aspects, the wash and suspension buffer described herein is not a hypertonic buffer. In some aspects, the wash and suspension buffer described herein is not a hypotonic buffer.
  • the kit further includes a cap configured to seal the inlet of the removable insert.
  • the invention features a device for lysing biological particles that includes a flow path having an inlet; an outlet; and at least one feature with a corner radius of less than about 1 mm disposed in the flow path.
  • the flow path includes a plurality of features, each feature having a corner radius of less than about 1 mm and disposed in the flow path.
  • At least two of the features are positioned in register and on opposite sides of the flow path.
  • the plurality of features are arranged in a sawtooth pattern.
  • the device includes a plurality of flow paths, each flow path having an inlet; an outlet; and at least one feature with a corner radius of less than about 1 mm disposed in the flow path.
  • the plurality of flow paths are substantially parallel.
  • the device further includes a filter positioned in the flow path at or upstream of the outlet and configured to trap particles of a predetermined size.
  • the invention features a kit that includes a vessel and a device for lysing biological particles that includes a flow path having an inlet; an outlet; and at least one feature with a corner radius of less than about 1 mm disposed in the flow path.
  • the device is configured to fit in the vessel.
  • the kit further includes a cap configured to seal the inlet of the device.
  • the flow path includes a plurality of features, each feature having a corner radius of less than about 1 mm and disposed in the flow path. In some embodiments, at least two of the features are positioned in register and on opposite sides of the flow path.
  • the plurality of features are arranged in a sawtooth pattern.
  • the device includes a plurality of flow paths, each flow path having an inlet; an outlet; and at least one feature with a corner radius of less than about 1 mm disposed in the flow path.
  • the plurality of flow paths are substantially parallel.
  • the kit further includes a filter positioned in the flow path at or upstream of the outlet and configured to trap particles of a predetermined size.
  • the invention features a method for lysing biological particles.
  • the method includes providing a device including a flow path having an inlet and an outlet, the flow path having at least one feature with a corner radius of less than about 1 mm and disposed in the flow path.
  • the method further includes flowing a liquid mixture including the biological particles through the flow path.
  • the at least one feature lyses the biological particles, and at least a portion of the biological particles or the contents thereof exit the flow path via the outlet.
  • the method further includes washing the biological particles in the flow path.
  • the method further includes providing magnetic particles that bind to at least a portion of the biological particles or the contents thereof.
  • the invention features a method for lysing biological particles.
  • the method includes providing a vessel and a device having a flow path with an inlet and an outlet, the flow path including at least one feature with a corner radius of less than about 1 mm and disposed in the flow path, wherein the device is positioned in the vessel.
  • the method further includes providing a liquid mixture including the biological particles to the inlet of the device and centrifuging the device in the vessel. Upon centrifugation, the at least one feature lyses the biological particles, and at least a portion of the biological particles or the contents thereof exit the flow path via the outlet and are collected in the vessel.
  • the invention features a kit that includes a vessel and a device being configured to fit in the vessel.
  • the device includes an inlet; an outlet; and a filter positioned in the device at or upstream of the outlet and configured to trap particles of a predetermined size.
  • the device further includes a layer that includes a flow path with at least one feature with a corner radius of less than about 1 mm and disposed in the flow path.
  • the layer is disposed at or upstream of the outlet (e.g., upstream or downstream of the filter).
  • the layer includes a plurality of flow paths, each flow path in the layer having an inlet; an outlet; and at least one feature with a corner radius of less than about 1 mm disposed in the flow path.
  • the plurality of flow paths in the layer are substantially parallel.
  • the vessel includes a medium having a density of greater than 1.0 g/m.
  • the invention features a method for purifying a second subset of biological particles using a kit as described herein.
  • the method includes providing the kit, providing a liquid mixture with biological particles to the inlet of the device; and centrifuging the device in the vessel. A first subset of the biological particles is trapped by the filter, and a second subset of the biological particles exits the outlet and is collected in the vessel.
  • the vessel includes a medium having a density of greater than 1 .0 g/m, and the second subset of biological particles is in the medium, e.g., pelleted during centrifugation.
  • the invention features a method for lysing biological particles using a kit as described herein that includes a device (e.g., having a layer with a flow path having at least one feature with a corner radius of less than about 1 mm disposed in the flow path) and a vessel to house the device.
  • the method includes providing the kit, providing a liquid mixture with biological particles to the inlet of the device; and centrifuging the device in the vessel.
  • the at least one feature lyses the biological particles, and at least a portion of the contents of the biological particles exits the flow path via the outlet and is collected in the vessel.
  • the invention features a kit for lysing biological particles.
  • the kit includes a vessel that includes a plurality of features having a corner radius of less than about 1 mm disposed along a wall of the vessel.
  • the kit further includes a pestle configured to fit within the vessel.
  • the pestle may include a plurality of features having a corner radius of less than about 1 mm disposed along a wall of the pestle.
  • the plurality of features of the vessel and/or the plurality of features of the pestle is arranged in a sawtooth pattern.
  • the invention features a method of lysing biological particles.
  • the method includes providing a kit of as described herein; providing a liquid mixture including the biological particles in the vessel; and rotating the pestle in the vessel.
  • the plurality of features of the vessel and/or the plurality of features of the pestle lyse the biological particles.
  • adaptor(s),” “adapter(s),” and “tag(s)” may be used synonymously.
  • An adaptor or tag can be coupled to a polynucleotide sequence to be “tagged” by any approach including ligation, hybridization, or other approaches.
  • barcode generally refers to a label, or identifier, that conveys or is capable of conveying information about an analyte.
  • a barcode can be part of an analyte.
  • a barcode can be a tag attached to an analyte (e.g., nucleic acid molecule) or a combination of the tag in addition to an endogenous characteristic of the analyte (e.g., size of the analyte or end sequence(s)).
  • a barcode may be unique. Barcodes can have a variety of different formats.
  • barcodes can include: polynucleotide barcodes; random nucleic acid and/or amino acid sequences; and synthetic nucleic acid and/or amino acid sequences.
  • a barcode can be attached to an analyte in a reversible or irreversible manner.
  • a barcode can be added to, for example, a fragment of a deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sample before, during, and/or after sequencing of the sample. Barcodes can allow for identification and/or quantification of individual sequencing-reads in real time.
  • the term “support,” as used herein, generally refers to a particle that is not a biological particle.
  • the particle may be a solid or semi-solid particle.
  • the particle may be a bead, such as a gel bead.
  • the gel bead may include a polymer matrix (e.g., matrix formed by polymerization or cross-linking).
  • the polymer matrix may include one or more polymers (e.g., polymers having different functional groups or repeat units). Polymers in the polymer matrix may be randomly arranged, such as in random copolymers, and/or have ordered structures, such as in block copolymers. Cross-linking can be via covalent, ionic, or inductive, interactions, or physical entanglement.
  • the bead may be a macromolecule.
  • the bead may be formed of nucleic acid molecules bound together.
  • the bead may be formed via covalent or non-covalent assembly of molecules (e.g., macromolecules), such as monomers or polymers.
  • Such polymers or monomers may be natural or synthetic.
  • Such polymers or monomers may be or include, for example, nucleic acid molecules (e.g., DNA or RNA).
  • the bead may be formed of a polymeric material.
  • the bead may be magnetic or non-magnetic.
  • the bead may be rigid.
  • the bead may be flexible and/or compressible.
  • the bead may be disruptable or dissolvable.
  • the bead may be a solid particle (e.g., a metal-based particle including but not limited to iron oxide, gold or silver) covered with a coating comprising one or more polymers. Such coating may be disruptable or dissolvable.
  • the term “biological particle,” as used herein, generally refers to a discrete biological system derived from a biological sample.
  • the biological particle may be a virus.
  • the biological particle may be a cell or derivative of a cell.
  • the biological particle may be an organelle from a cell. Examples of an organelle from a cell include, without limitation, a nucleus, endoplasmic reticulum, a ribosome, a Golgi apparatus, an endoplasmic reticulum, a chloroplast, an endocytic vesicle, an exocytic vesicle, a vacuole, and a lysosome.
  • the biological particle may be a rare cell from a population of cells.
  • the biological particle may be any type of cell, including without limitation prokaryotic cells, eukaryotic cells, bacterial, fungal, plant, mammalian, or other animal cell type, mycoplasmas, normal tissue cells, tumor cells, or any other cell type, whether derived from single cell or multicellular organisms.
  • the biological particle may be a constituent of a cell.
  • the biological particle may be or may include DNA, RNA, organelles, proteins, or any combination thereof.
  • the biological particle may be or may include a matrix (e.g., a gel or polymer matrix) comprising a cell or one or more constituents from a cell (e.g., cell bead), such as DNA, RNA, organelles, proteins, or any combination thereof, from the cell.
  • the biological particle may be obtained from a tissue of a subject.
  • the biological particle may be a hardened cell. Such hardened cell may or may not include a cell wall or cell membrane.
  • the biological particle may include one or more constituents of a cell, but may not include other constituents of the cell. An example of such constituents is a nucleus or another organelle of a cell.
  • a cell may be a live cell.
  • the live cell may be capable of being cultured, for example, being cultured when enclosed in a gel or polymer matrix, or cultured when comprising a gel or polymer matrix.
  • the term “fluidically connected,” as used herein, refers to a direct connection between at least two device elements, e.g., a channel, reservoir, etc., that allows for fluid to move between such device elements without passing through an intervening element.
  • the term “genome,” as used herein, generally refers to genomic information from a subject, which may be, for example, at least a portion or an entirety of a subject’s hereditary information.
  • a genome can be encoded either in DNA or in RNA.
  • a genome can comprise coding regions that code for proteins as well as non-coding regions.
  • a genome can include the sequence of all chromosomes together in an organism. For example, the human genome has a total of 46 chromosomes. The sequence of all of these together may constitute a human genome.
  • in fluid communication with refers to a connection between at least two device elements, e.g., a channel, reservoir, etc., that allows for fluid to move between such device elements with or without passing through one or more intervening device elements.
  • a pair of sharp features that are in register may have the tips of the sharp features substantially aligned on opposite sides of a flow path, e.g., the tips may be offset by no more than 50 pm, e.g., no more than 40, 30, 20, 10, 5, or 1 pm.
  • a device with a plurality of sharp features positioned on opposite sides of the flow path may have multiple matched pairs where the tips of the sharp features of each matched pair are substantially aligned on opposite sides of the flow path.
  • the macromolecular constituent may comprise a nucleic acid.
  • the biological particle may be a macromolecule.
  • the macromolecular constituent may comprise DNA or a DNA molecule.
  • the macromolecular constituent may comprise RNA or an RNA molecule.
  • the RNA may be coding or non-coding.
  • the RNA may be messenger RNA (mRNA), ribosomal RNA (rRNA) or transfer RNA (tRNA), for example.
  • the RNA may be a transcript.
  • the RNA molecule may be (i) a clustered regularly interspaced short palindromic (CRISPR) RNA molecule (crRNA) or (ii) a single guide RNA (sgRNA) molecule.
  • CRISPR CRISPR
  • crRNA clustered regularly interspaced short palindromic
  • sgRNA single guide RNA
  • the RNA may be small RNA that are less than 200 nucleic acid bases in length, or large RNA that are greater than 200 nucleic acid bases in length.
  • Small RNAs may include 5.8S ribosomal RNA (rRNA), 5S rRNA, transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA) and small rDNA-derived RNA (srRNA).
  • the RNA may be double-stranded RNA or single-stranded RNA.
  • the RNA may be circular RNA.
  • the macromolecular constituent may comprise a protein.
  • the macromolecular constituent may comprise a peptide.
  • the macromolecular constituent may comprise a polypeptide or a protein.
  • the polypeptide or protein may be an extracellular or an intracellular polypeptide or protein.
  • the macromolecular constituent may also comprise a metabolite.
  • the term “molecular tag,” as used herein, generally refers to a molecule capable of binding to a macromolecular constituent.
  • the molecular tag may bind to the macromolecular constituent with high affinity.
  • the molecular tag may bind to the macromolecular constituent with high specificity.
  • the molecular tag may comprise a nucleotide sequence.
  • the molecular tag may comprise an oligonucleotide or polypeptide sequence.
  • the molecular tag may comprise a DNA aptamer.
  • the molecular tag may be or comprise a primer.
  • the molecular tag may be or comprise a protein.
  • the molecular tag may comprise a polypeptide.
  • the molecular tag may be a barcode.
  • oil generally refers to a liquid that is not miscible with water.
  • An oil may have a density higher or lower than water and/or a viscosity higher or lower than water.
  • partate component of a cell refers to a discrete biological system derived from a cell or fragment thereof and having at least one dimension of 0.01 pm (e.g., at least 0.01 pm, at least 0.1 pm, at least 1 pm, at least 10 pm, or at least 100 pm).
  • a particulate component of a cell may be, for example, an organelle, such as a nucleus, an exosome, a liposome, an endoplasmic reticulum (e.g., rough or smooth), a ribosome, a Golgi apparatus, a chloroplast, an endocytic vesicle, an exocytic vesicle, a vacuole, a lysosome, or a mitochondrion.
  • an organelle such as a nucleus, an exosome, a liposome, an endoplasmic reticulum (e.g., rough or smooth), a ribosome, a Golgi apparatus, a chloroplast, an endocytic vesicle, an exocytic vesicle, a vacuole, a lysosome, or a mitochondrion.
  • sample generally refers to a biological sample of a subject.
  • the biological sample may be a nucleic acid sample or protein sample.
  • the biological sample may be derived from another sample.
  • the sample may be a tissue sample, such as a biopsy, core biopsy, needle aspirate, or fine needle aspirate.
  • the sample may be a liquid sample, such as a blood sample, urine sample, or saliva sample.
  • the sample may be a skin sample.
  • the sample may be a cheek swap.
  • the sample may be a plasma or serum sample.
  • the sample may include a biological particle, e.g., a cell or virus, or a population thereof, or it may alternatively be free of biological particles.
  • a cell-free sample may include polynucleotides. Polynucleotides may be isolated from a bodily sample that may be selected from the group consisting of blood, plasma, serum, urine, saliva, mucosal excretions, sputum, stool and tears.
  • sequence of nucleotide bases in one or more polynucleotides generally refers to methods and technologies for determining the sequence of nucleotide bases in one or more polynucleotides.
  • the polynucleotides can be, for example, nucleic acid molecules such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), including variants or derivatives thereof (e.g., single stranded DNA). Sequencing can be performed by various systems currently available, such as, without limitation, a sequencing system by ILLUMINA®, Pacific Biosciences (PACBIO®), Oxford NANOPORE®, or Life Technologies (ION TORRENT®).
  • sequencing may be performed using nucleic acid amplification, polymerase chain reaction (PCR) (e.g., digital PCR, quantitative PCR, or real time PCR), or isothermal amplification.
  • PCR polymerase chain reaction
  • Such systems may provide a plurality of raw genetic data corresponding to the genetic information of a subject (e.g., human), as generated by the systems from a sample provided by the subject.
  • sequencing reads also “reads” herein).
  • a read may include a string of nucleic acid bases corresponding to a sequence of a nucleic acid molecule that has been sequenced.
  • systems and methods provided herein may be used with proteomic information.
  • subject generally refers to an animal, such as a mammal (e.g., human) or avian (e.g., bird), or other organism, such as a plant.
  • the subject can be a vertebrate, a mammal, a mouse, a primate, a simian or a human. Animals may include, but are not limited to, farm animals, sport animals, and pets.
  • a subject can be a healthy or asymptomatic individual, an individual that has or is suspected of having a disease (e.g., cancer) or a pre-disposition to the disease, or an individual that is in need of therapy or suspected of needing therapy.
  • a subject can be a patient.
  • substantially stationary as used herein with respect to droplet or particle formation, generally refers to a state when motion of formed droplets or particles in the continuous phase is passive, e.g., resulting from the difference in density between the dispersed phase and the continuous phase.
  • FIG. 1 is a schematic diagram of a kit of the invention.
  • the kit includes an outer vessel and a removable insert configured to fit in the vessel.
  • the removable insert includes an inlet and a thixotropic layer that separates liquid layers with different densities.
  • FIG. 2 is a schematic diagram of a method as described herein.
  • a vessel containing a liquid mixture with a suspension of biological particles and debris is centrifuged. The supernatant liquid is discarded, and the biological particles are resuspended in a new liquid without debris.
  • FIG. 3 is a schematic diagram of a device as described herein.
  • the device includes a plurality of flow paths containing sharp features configured to lyse a cell as it passes through the flow path. Upon lysis, the contents of the cell, such as cytoplasmic RNA and nuclei, are released from the cell.
  • FIG. 4 is a schematic diagram of a device as in FIG. 3 and further includes a filter configured to trap particles of a predetermined size.
  • FIG. 5 is a schematic diagram of a device as in FIG. 3 that further includes a plurality of magnetic particles configured to bind to and trap certain biological material, such as cytoplasmic RNA.
  • FIGS. 6A and 6B are schematic diagrams of cross-sections of a device and correspond to cross-section A and cross-section B as shown in FIGS. 3 and 5.
  • FIG. 6A shows intact cells
  • FIG. 6B shows lysed cells.
  • FIG. 7 is a schematic diagram showing a kit that includes a device including a plurality of flow paths containing sharp features configured to lyse a cell as it passes through the flow path.
  • the device is configured to fit within a vessel and contains a cap that seals the inlet of the device. Upon centrifugation, the cells are ruptured, and nuclei collect at the bottom of the vessel.
  • FIG. 8 is a schematic diagram showing a closeup view of the device in the kit of FIG. 7.
  • FIG. 9 is a schematic drawing showing a kit and method as described herein.
  • the kit includes a device and a vessel and is configured to collect biological particles.
  • the device contains a polymer filter and a vessel containing a dense media that collects biological particles. Shown on the left is the vessel with a suspension of biological particles.
  • the kit can then be centrifuged, vortexed, and centrifuged again to collect a pellet of the biological particles as shown on the right.
  • FIG. 10 is a schematic drawing showing a kit as described herein containing a device that fits within a vessel.
  • the device includes a layer of textured channels (e.g., containing sharp features) configured to lyse the biological particles.
  • the device further includes a filter layer (e.g., porous filter) and an outlet to allow the contents of the biological particles (e.g., nuclei) to collect in the vessel.
  • the vessel further includes a dense media to collect the biological particles.
  • FIG. 11 is a schematic drawing showing a kit as described herein.
  • the kit contains a textured pestle and a textured lysis column (e.g., containing sharp features). The pestle fits within the column and can be rotated to lyse biological particles.
  • FIG. 12 depicts the fraction of nucleic acid reads in cells for the presently described nuclei isolation methods of Example 1 versus a widely adopted homebrew nuclei isolation protocol (left); and a violin plot (right) comparing the median number of genes per cell identified in cells using the methods of Example 1 versus a widely adopted homebrew nuclei isolation protocol.
  • the presently described methods improves data yield by about 40% and increases the complexity, in terms of numbers of genes captured, by about 20%.
  • the samples were frozen mouse kidney tissue.
  • FIG. 13 demonstrates that the presently described nuclei isolation methods of Example 1 is an improvement over the known nuclei isolation protocols with adult mouse kidney tissue (left) and human kidney cancer tissue (right), wherein the nuclei isolation kit data point is the presently described nuclei isolation protocol.
  • the present nuclei isolation method results in a higher signal to noise ratio over other methods, even with more necrotic tissues like cancer samples.
  • the presently described nuclei isolation methods improve data yields by at least about 15% in comparison to the Salty EZ lysis methods and 40% better than a simple nuclei sorted sample method.
  • Salty EZ method is the Salty-EZ10 protocol.
  • FIG. 14 demonstrates that the presently described nuclei isolation methods yield increased unique molecular identifiers (UMIs) and genes detected (-20% increase) in from mouse kidney and human kidney cancer tissues.
  • UMIs unique molecular identifiers
  • FIG. 15 demonstrates that the presently described nuclei isolation methods provide ample debris cleanup in samples that comprise myelin and other complex debris.
  • the “Chromium Nuclei Isolation” panel provides a microscopic view of the final sample after the nuclei isolation method of the present disclosure has been performed, as compared to the “Sample after dissociation” microscopy panel. Furthermore, simply filtering the sample immediately post dissociation does not provide sufficient debris cleanup for the nuclei isolation as can be seen in the “after filtering” microscopy panel. While some degree is acceptable, large particles of varying sizes are sure to clog microfluidics channels needed for downstream single cell analysis of the nuclei.
  • FIG. 16 demonstrates that the cells do not need to be exclusively from organized dense tissues, they can be in suspensions, such a previously dissociated cells or cultured cells or non-adherent cells that do not grow/organize as a three dimensional tissue.
  • the figure is the result of dissociated tumor cells processed with the nuclei isolation methods described herein versus starting with solid tumor tissue of the same type.
  • the figure demonstrates that the barcode rank for UMI counts for the cell suspension align tightly with the same for just cells alone.
  • FIG. 17 demonstrates that the complexity (as measured by median genes per cell and median UMIs per cell) of single cell analysis data yielded by nuclei isolated from a cell suspension of dissociated tumor cells versus cells of dissociated tumor tissue (nuclei from suspended cells vs. suspended cells) are statistically insignificant from one another - meaning that utilizing nuclei from cell suspensions yields a very similar complexity as measured by median genes/UMIs per cell.
  • kits for purifying or lysing biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • the methods, devices, and kits may be used to purify biological particles of a desired property and/or size.
  • the purified biological particles may then be suitable for incorporation into droplets or particles that may be used as microscale chemical reactors, e.g., for genetic sequencing.
  • the kits described herein include a vessel that includes an inlet and a thixotropic layer disposed in the vessel.
  • the vessel may further include an outlet to allow flow therethrough.
  • An outer vessel can be used to collect liquid that passes through the outlet, e.g., following centrifugation.
  • a device or kit as described herein include a flow path with one or more features (e.g., sharp features) that are configured to lyse a biological particle (e.g., a cell or particulate component thereof, e.g., nucleus) to separate or purify biological particles or the contents thereof.
  • a biological particle e.g., a cell or particulate component thereof, e.g., nucleus
  • the invention can provide purified populations of biological particles (e.g., cells or particulate components thereof, e.g., organelles, such as nuclei).
  • Tissue storage solutions only provide short-term storage, generally about 72 hours or less, and the resulting viability post-storage is very sample dependent.
  • Tissue cryopreservation requires tissues to be cut up into very small pieces, which isn’t feasible if there is interest in tissue morphology. Flash-freezing tissue is the most used method besides formalin/formaldehyde fixation.
  • Nuclei isolate can be a superior method over preserving or quickly processing tissue as: (1) some samples cannot be easily dissociated into single cells but can be prepared by isolating nuclei from a variety of tissues, including frozen tissue; (2) nuclei isolation avoids the loss of cells that are often list during fresh tissue dissociation such as neurons and adipocytes and avoids long enzymatic incubations that can alter gene expression and create cell-type biases such as what occurs with glial activation; and it enables accessing transcriptional and epigenetic information - nuclei contain lots of unspliced mFtNA and chromatin, and profiling of gene expression and chromatin structure can vbe used to define cell stages, lineage tracing, and better understanding of gene regulation.
  • the devices, kits, and methods described herein provide various advantages over other available devices and techniques known in the art.
  • the devices, kits, and methods described herein may remove background (e.g., cytoplasmic) RNA and DNA, remove dead cells (e.g., provide samples with high cell viability), remove cellular debris, remove clumps and cell doublets, and remove poor quality nuclei.
  • the devices, kits, and methods improve the quality of a preparation of biological particles, e.g., cells or nuclei, wherein higher quality preparation generally minimize the presence of debris from lysed cells or non-intact nuclei. For example, quality can be assessed by cell viability measurement protocols.
  • Viability can be assessed by staining (e.g., with Trypan blue) of a preparation followed by counting (e.g., automated counter or hemocyto meter) of biological particles. Viability can be determined by measuring non-lysed cells that exclude staining, e.g., Trypan blue, while nuclei can be measured as not excluding staining. Alternatively, nuclei can be measured by fluorescent dyes, e.g., ethidium homodimer-1 , may be used to measure and distinguish nuclei from debris. In addition, high quality nuclei can be measured by visualization with microscopy. High quality nuclei preparations are characterized by nuclei that are clump-free and debris-free nuclei, and/or have intact membranes that are smooth and round.
  • a high-quality nuclei preparation after cell lysis is demonstrated by measuring about less than 1% to about less than 10% live input cells. In other embodiments, a high-quality nuclei preparation after cell lysis is demonstrated by measuring about less than 1%, about less than 2%, about less than 3%, about less than 4%, about less than 5%, about less than 6% to about less than 7% live input cells, about less than 8%, about less than 9%, or about less than 10% live input cells.
  • the device or kit does not activate, deactivate, or change gene expression, viability, or functionality of the biological particles (e.g., cells or particulate components thereof, e.g., nuclei).
  • the biological particles e.g., cells or particulate components thereof, e.g., nuclei.
  • This feature is particularly important when working with fixed or frozen cells or organelles (e.g., nuclei). Therefore, the samples being analyzed are not tainted by biological particles with altered expression patterns or alternative cellular subtypes. Other techniques are harsh, which reduces the efficiency of sample preparation.
  • the devices and kits described herein reduce loss and provide enhanced purification, thereby providing a higher yield and increased purity of biological particles (e.g., cells or particulate components thereof, e.g., nuclei) for use in subsequent steps.
  • biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • Other features and advantages of the invention as a whole are provided in the examples.
  • a kit for purifying biological particles includes a vessel with an inlet to which a liquid can be provided.
  • the vessel further includes a thixotropic layer disposed in the vessel (see FIG. 1).
  • the vessel may further include an outlet to allow liquid to flow out of the vessel, e.g., to an outer vessel.
  • the outer vessel can be used to collect liquid that passes through the outlet, e.g., following centrifugation.
  • the devices and kits described herein may include a vessel.
  • the vessel can be a removable insert that fits within an outer vessel.
  • the vessel may contain an outlet.
  • the vessel may contain a removable or breakable tip such that liquid can flow through the outlet and once the tip is removed.
  • the vessel may be any suitable geometry, such as cylindrical, conical, and the like.
  • the vessel may be, for example, a microcentrifuge tube or a PCR tube or a similar device that can be removably inserted within a microcentrifuge tube or a PCR tube.
  • the vessel may have a volume of e.g., 1 nl_ - 100 ml_ (e.g., 1 nl_,
  • the vessel may have a volume of less than about 10,000 mI_ (e.g., less than about 1 ,000 mI_, less than about 100 mI_, or less than about 10 mI_, e.g., from about 1 mI_ to about 10,000 mI_, from about 10 mI_ to about 10,000 mI_, from about 100 mI_, to about 10,000 mI_, from about 1 ,000 mI_ to about 10,000 mI_, from about 10 mI_ to about 5,000 mI_, from about 10 mI_ to about 1 ,000 mI_, from about 100 mI_ to about 1 ,000 mI_, from about 500 mI_ to about 1 ,000 mI_, from about 1 mI_ to about 1 ,000 mI_, from about 1 mI_ to about 500 mI_, from about 1 mI_ to about 100 mI_, from about 1 mI_ to about 50 mI
  • the vessel may have a thickness of from about 10 miti to about 10 mm (e.g., from about 10 miti to about 1 mm, from about 10 miti to about 100 miti, from about 50 miti to about 100 miti, from about 100 miti to about 10 mm, from about 1 mm to about 10 mm, from about 500 miti to about 1 mm, from about 1 mm to about 5 mm, from about 1 mm to about 2 mm, e.g., about 1 .5 mm).
  • the vessel may have thickness of from about 10 miti to about 100 miti, e.g., about 10 miti, 20 miti, 30 miti, 40 miti, 50 miti,
  • miti, 70 miti, 80 miti, 90 miti, or 100 miti e.g., from about 100 miti to about 1000 miti, e.g., about 200 miti, 300 miti, 400 miti, 500 miti, 600 miti, 700 miti, 800 miti, 900 miti, or 1000 miti, e.g., from about 1 mm to about 10 mm, e.g., 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, or 10 mm.
  • the vessel may contain a cap that covers and/or seals the vessel.
  • the cap can be attached to the vessel or a separate component.
  • the cap can fit on the inlet and cover the vessel during subsequent use, e.g., during centrifugation.
  • the vessel contains a thixotropic layer disposed within the vessel.
  • the thixotropic layer separate layers of liquid with different densities to allow separation and purification of biological particles.
  • the thixotropic layer may include a polymeric gel, such as a polyester.
  • the thixotropic layer may be disposed within the vessel to allow for effective separation of liquids with different densities.
  • the thixotropic layer may have a disc or cylindrical shape within the vessel.
  • the length, width, and height of the thixotropic layer may be at least, independently, e.g., 0.1 pm - 10 mm (e.g., 0.1-1 pm, e.g., 0.1 pm, 0.2 pm, 0.3 pm, 0.4 pm, 0.5 pm, 0.6 pm, 0.7 pm, 0.8 pm, 0.9 pm, 1 pm, e.g., 1-10 pm, e.g.,
  • the thixotropic layer may have a volume of e.g., 1 nl_ - 10 ml_ (e.g., 1 nl_, 2 nl_, 3 nl_, 4 nl_, 5 nl_, 6 nl_, 7 nl_, 8 nl_, 9 nl_, 10 nl_, e.g., 10 nL - 100 nl_, e.g., 20 nl_, 30 nl_, 40 nL, 50 nL, 60 nL, 70 nL, 80 nL, 90 nL, 100 nL, e.g., 100 nL - 1 pL, e.g., 200 nL, 300 nL, 400 nL, 500 nL, 600 nL, 700 nL, 800 nL, 900 nL, 1 pL, e.g., 1 pL - 10 pL,
  • the thixotropic layer may separate a first layer of liquid having a first density and a second layer of liquid having a second density, thereby forming a density gradient within the vessel.
  • the second liquid may have a density that is lower than the density of the first liquid.
  • the vessel may be loaded with a first layer of liquid having a first density.
  • the first layer may be disposed below the thixotropic layer.
  • the first layer may be positioned between the outlet and the thixotropic layer.
  • the first layer may include iodixanol.
  • the first layer may include from about 10% to about 50% iodixanol (e.g., from about 15% to about 45%, from about 20% to about 40%, from about 25% to about 35%, from about 26% to about 34%, from about 27% to about 33%, from about 28% to about 32 %, from about 29% to about 31%, from about 29.5% to about 30.5%, e.g., about 30%.
  • a device may include a centrifuge tube containing a liquid having a predetermined density that is composed of tissue culture medium.
  • the centrifuge tube may contain a liquid having tissue culture medium and a concentration of from about 10% to about 50% iodixanol (e.g., from about 15% to about 45%, from about 20% to about 35%, from about 22% to about 32%, or from about 24% to about 30%).
  • the centrifuge tube may be, for example, a microcentrifuge tube or a PCR tube, or any other suitable structure configured to fit within a centrifuge.
  • the density of the liquid is from about 1 .11 g/mL to about 1 .12 g/mL (e.g., from about 1 .146 g/mL to about 1 .175, e.g., about 1 .1107 g/mL, 1.117 g/mL, 1 .127 g/mL, 1 .136 g/mL, 1 .146 g/mL, 1 .156 g/mL, 1 .165 g/mL, or 1 .175 g/mL.
  • the liquid may contain iodixanol or a comparable component to create a similar density as iodixanol, such as ficoll, histopaque, or sucrose.
  • a liquid having tissue culture medium and the density described above allows easy removal of cellular debris, e.g., during centrifugation, while still maintaining viable conditions for the biological particles or particulate components thereof, e.g., nuclei.
  • the invention employs an outer vessel that to house the vessel and optionally to collect a liquid from the outlet of the vessel, e.g., that is a removable insert within the outer vessel.
  • the outer vessel may be any suitable geometry, such as cylindrical, conical, and the like.
  • the outer vessel may be, for example, a microcentrifuge tube or a PCR tube or a similar device configured to house a microcentrifuge tube or a PCR tube.
  • the outer vessel may have a volume may have a volume of e.g., 1 nL - 100 mL (e.g., 1 nL, 2 nL, 3 nL, 4 nL, 5 nL, 6 nL, 7 nL, 8 nL, 9 nL, 10 nL, e.g., 10 nL - 100 nL, e.g., 20 nL, 30 nL, 40 nL, 50 nL, 60 nL, 70 nL, 80 nL, 90 nL, 100 nL, e.g., 100 nL - 1 pL, e.g., 200 nL, 300 nL, 400 nL, 500 nL, 600 nL, 700 nL, 800 nL, 900 nL, 1 pL, e.g., 1 pL - 10 pL, e.g., 2 pL, 3 p
  • the outer vessel may have a volume of less than about 10,000 pL (e.g., less than about 1 ,000 pL, less than about 100 pL, or less than about 10 pL, e.g., from about 1 pL to about 10,000 pL, from about 10 pL to about 10,000 pL, from about 100 pL, to about 10,000 pL, from about 1 ,000 pL to about 10,000 pL, from about 10 pL to about 5,000 pL, from about 10 pL to about 1 ,000 pL, from about 100 pL to about 1 ,000 pL, from about 500 pL to about 1 ,000 pL, from about 1 pL to about 1 ,000 pL, from about 1 pL to about 500 pL, from about 1 pL to about 100 pL, from about 1 pL to about 50 pL, or from about 1 pL to about 10 pL).
  • 10,000 pL e.g.
  • the outer vessel may have a volume that is the same or greater than the removable insert.
  • the outer vessel may have a thickness of from about 10 miti to about 10 mm (e.g., from about 10 miti to about 1 mm, from about 10 miti to about 100 miti, from about 50 miti to about 100 miti, from about 100 miti to about 10 mm, from about 1 mm to about 10 mm, from about 500 miti to about 1 mm, from about 1 mm to about 5 mm, from about 1 mm to about 2 mm, e.g., about 1 .5 mm).
  • 10 miti to about 10 mm e.g., from about 10 miti to about 1 mm, from about 10 miti to about 100 miti, from about 50 miti to about 100 miti, from about 100 miti to about 10 mm, from about 1 mm to about 10 mm, from about 500 miti to about 1 mm, from about 1 mm to about 5 mm, from about 1 mm to about 2 mm, e
  • the vessel may have thickness of from about 10 miti to about 100 miti, e.g., about 10 miti, 20 miti, 30 miti, 40 miti, 50 miti, 60 miti, 70 miti, 80 miti, 90 miti, or 100 miti, e.g., from about 100 miti to about 1000 miti, e.g., about 200 miti, 300 miti, 400 miti, 500 miti, 600 miti, 700 miti, 800 miti, 900 miti, or 1000 miti, e.g., from about 1 mm to about 10 mm, e.g., 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, or 10 mm.
  • the outer vessel may contain a cap that covers and/or seals the outer vessel.
  • the cap can be attached to the outer vessel or may be a separate component.
  • the cap can fit on the inlet of the outer vessel and cover the outer vessel after use, e.g., for storage of the components therein.
  • the outer vessel may include a medium having a density of greater than about 1 .0 g/m, e.g., to collect biological particles or the contents thereof.
  • the medium has a density from about 1 .11 g/mL to about 1 .12 g/mL (e.g., from about 1 .146 g/mL to about 1 .175, e.g., about 1 .1107 g/ml_, 1.117 g/mL, 1 .127 g/mL, 1 .136 g/mL, 1 .146 g/mL, 1 .156 g/mL, 1 .165 g/mL, or 1 .175 g/mL.
  • the liquid may contain iodixanol or a comparable component to create a similar density as iodixanol, such as ficoll, histopaque, or sucrose.
  • Another embodiment of a device as described herein for lysing, separating, or purifying biological particles includes a flow path having an inlet, an outlet, and a filter and/or at least one feature with a corner radius of less than about 10 mm, e.g., less than about 1 mm, disposed in the flow path.
  • the sharp feature may have a corner radius of less than about 10 mm (e.g., less than about 9 mm, 8 mm, 7 mm, 6 mm, 5 mm, 4 mm, 3 mm, 2 mm, or 1 mm, e.g., less than about 990 pm, 980 pm, 970 pm, 960 pm, 950 pm, 940 pm, 930 pm, 920 pm, 910 pm, or 900 pm, e.g., less than about 800 pm, 700 pm, 600 pm, 500 pm, 400 pm, 300 pm, 200 pm, or 100 pm, e.g., less than about 90 pm, 80 pm, 70 pm, 60 pm, or 50 pm, e.g., less than about 45 pm, 40 pm, 35 pm, 30 pm, 25 pm, 20 pm, 15 pm, or 10 pm, e.g., less than about 9 pm, 8 pm, 7 pm, 6 pm, 5 pm, 4 pm, 3 pm, 2 pm or 1 pm, e.g., from about 10 mm (e
  • the device includes at least two sharp features, e.g., each with a corner radius of less than about 10 mm, e.g., less than about 1 mm.
  • the device may have at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, or more sharp features disposed within the flow path.
  • the sharp feature(s) disposed within the flow path allows the device to lyse a biological particle (e.g., a cell or particulate component thereof, e.g., an organelle, such as a nucleus) as it passes over the sharp feature (FIG. 3).
  • the sharp feature may have a polygonal shape.
  • a cross-section of the feature may be a polygon with 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, or more sides.
  • the vertices of the polygon may have a corner radius of less than about 10 mm, e.g., less than about 1 mm.
  • the device may include a protrusion with a plurality of sharp features or a plurality of protrusions, each having a sharp feature.
  • the device includes a plurality of sharp features disposed in the flow path.
  • the plurality of features may be arranged, for example, in a sawtooth pattern.
  • the features are positioned on opposite sides of the flow path (e.g., in register) in order to create narrow regions through which the biological particles pass through to increase the probability of being lysed (FIGS. 6A and 6B).
  • the device includes a plurality of matched pairs of features disposed in the flow path where each matched pair is in register.
  • the sharp features may be spaced apart, e.g., at predetermined intervals.
  • the sharp features e.g., of a sawtooth pattern
  • the sharp features may be spaced from about 1 pm to about 1 cm apart, e.g., from about 1 pm to 10 pm, e.g., 2 pm, 3 pm, 4 pm, 5 pm, 6 pm, 7 pm, 8 pm, 9 pm, or 10 pm, e.g., from about 10 pm to about 100 pm, e.g., 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, or 100 pm, e.g., from about 100 pm to about 1 mm, e.g., 200 pm, 300 pm, 400 pm, 500 pm, 600 pm, 700 pm, 800 pm, 900 pm, or 1000 pm, e.g., 1 mm to about 10 mm, e.g., 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm
  • the sharp features are arranged in a pattern, such as a linear pattern or a grid pattern (e.g., with regularly spaced intervals therebetween).
  • the distance between the sharp features on opposite sides of the flow path are spaced apart, e.g., at predetermined intervals.
  • the spacing may be configured to match a size of a biological particle to be lysed.
  • the distance between sharp features on opposite sides of the flow path may be less than the diameter of a cell or a particular component thereof, e.g., a nucleus, e.g., to allow for efficient lysis upon contact with the sharp features.
  • the sharp features are spaced on opposite sides of the flow path from about 1 pm to about 1 mm apart, e.g., from about 1 pm to 10 pm, e.g., 2 pm, 3 pm, 4 pm, 5 pm, 6 pm, 7 pm, 8 pm, 9 pm, or 10 pm, e.g., from about 10 pm to about 100 pm, e.g., 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, or 100 pm, e.g., from about 100 pm to about 1 mm, e.g., 200 pm, 300 pm, 400 pm, 500 pm, 600 pm, 700 pm, 800 pm, 900 pm, or 1000 pm.
  • the device includes a plurality of flow paths, each flow path having an inlet, and outlet, and at least one sharp features with a corner radius of less than about 10 mm, e.g., less than about 1 mm, disposed in the flow path.
  • the plurality of flow paths may be substantially parallel (FIG. 3).
  • the plurality of flow paths may each have a plurality of sharp features.
  • the device includes a filter positioned in the flow path at or upstream of the outlet and configured to trap particles (e.g., biological particles) of a predetermined size (FIGS. 4 and 9).
  • the filter may function to trap large biological particles (e.g., cells) or tissue particles, e.g., prior to coming into contact with sharp features.
  • the device includes a filter, e.g., as described herein, and a layer that includes a flow path having a sharp feature, e.g., with a corner radius of less than about 10 mm, e.g., less than about 1 mm, as described herein (FIG. 10).
  • the layer may be disposed upstream or downstream of the filter.
  • the layer may include a plurality of flow paths, e.g., in substantially parallel orientation.
  • the flow path includes a plurality of sharp features.
  • the device may include a medium having a density of greater than about 1 .0 g/m, e.g., to collect biological particles or the contents thereof.
  • the filter may include a polymer, e.g., a solid polymeric structure.
  • the filter may include polyethylene or polyethylene derivatives, cyclic olefin copolymers (COC), polymethylmethacrylate (PMMA), polydimethylsiloxane (PDMS), polycarbonate, polystyrene, polypropylene, polyvinyl chloride, polytetrafluoroethylene, polyoxymethylene, polyether ether ketone, polycarbonate, polystyrene, or the like.
  • the filter is a porous filter.
  • the average pore size of the filter is about 5 pm to about 100 pm. In some aspects, the average pore size of the filter is about 5 pm, about 10 pm, about 15 pm about 20 pm, about 25 pm about 30 pm, about 35 pm, about 40 pm, about 45 pm, about 50 pm, about 55 pm, about 60 pm, about 65 pm, about 70 pm, about 75 pm, about 80 pm, about 85 pm, about 90 pm, about 95 pm, or about 100 pm.
  • the average pore size of the filter is about 5 pm to about 90 pm, about 5 pm to about 80 pm, about 5 pm to about 70 pm, about 5 pm to about 60 pm, about 5 pm to about 50 pm, about 5 pm to about 40 pm, about 5 pm to about 30 pm, about 5 pm to about 20 pm, about 5 pm to about 10 pm, about 10 pm to about 100 pm, about 10 pm to about 80 pm, about 10 pm to about 60 pm, about 10 pm to about 40 pm, about 10 pm to about 20 pm, about 20 pm to about 100 pm, about 20 pm to about 100 pm, about 20 pm to about 80 pm, about 20 pm to about 60 pm, about 20 pm to about 40 pm, about 30 pm to about 100 pm, about 30 pm to about 80 pm, about 30 pm to about 60 pm, about 30 pm to about 40 pm, about 40 pm to about 100 pm, about 40 pm to about 80 pm, about 40 pm to about 60 pm, about 50 pm to about 100 pm, about 50 pm to about 80 pm, about 50 pm to about 60 pm, about 60 pm to about 100 pm, about 60 pm, about
  • the filter comprises a thickness of about 0.2 mm to about 30 mm. In some aspects, the the filter comprises a thickness of about 0.2 mm, about 0.3 mm, about 0.4 mm, about 0.5 mm, about 1 mm, about 2 mm, about 3 mm, about 4 mm, about 5 mm, about 6 mm, about 7 mm, about 8 mm, about 9 mm, about 10 mm, about 11 mm, about 12 mm, about 13 mm, about 14 mm, about 15 mm, about 16 mm, about 17 mm, about 18 mm, about 19 mm, about 20 mm, about 21 mm, about 22 mm, about 23 mm, about 24 mm, about 25 mm, about 26 mm, about 27 mm, about 28 mm, about 29 mm, or about 30 mm.
  • the filter comprises a thickness of about 0.5 to about 30 mm, about 0.5 to about 25 mm, about 0.5 mm to about 20 mm, about 0.5 mm to about 15 mm, about 0.5 mm to about 10 mm, about 0.5 mm to about 5 mm, about 0.5 mm to about 1 mm, about 1 to about 30 mm, about 1 to about 25 mm, about 1 mm to about 20 mm, about 1 mm to about 15 mm, about 1 mm to about 10 mm, about 1 mm to about 5 mm, about 5 to about 30 mm, about 5 to about 25 mm, about 5 mm to about 20 mm, about 5 mm to about 15 mm, about 5 mm to about 10 mm, about 10 to about 30 mm, about 10 to about 25 mm, about 10 mm to about 20 mm, about 10 mm to about 15 mm, about 15 to about 30 mm, about 15 to about 25 mm, about 15 mm to about 20 mm, about 20 to about 30 mm, about 15
  • the filter is a polymer. In some aspect the filter is fibrous, in some aspects, the filter is a matrix. In some aspects, the filter is hydrophobic. In some aspects, the filter is coated in a hydrophobic coating. In some aspects, the filter is hydrophilic. In some aspects, the filter is coated in a hydrophilic coating.
  • the device with sharp feature(s) is employed in a kit in which the device is configured to fit within a vessel (e.g., an outer vessel) as described herein (see, e.g., FIGS. 7, 8 and 10).
  • the vessel may be any suitable geometry, such as cylindrical, conical, and the like.
  • the outer vessel may be, for example, a microcentrifuge tube or a PCR tube or a similar device. The vessel collects the liquid as it exits the outlet of the flow path.
  • the device is positioned in the outer vessel (e.g., microcentrifuge tube).
  • the outer vessel may contain a liquid having a density that is greater than the density of the mixture that is provided to the device (e.g., greater than 1.0 g/m).
  • kits for lysing biological particles includes a vessel that includes at least one sharp feature (e.g., a plurality of features) having a corner radius of less than about 10 mm, , e.g., less than about 1 mm, as described herein, disposed along a wall of the vessel.
  • the kit further includes a pestle configured to fit within the vessel.
  • the pestle may include at least one feature (e.g., a plurality of features) having a corner radius of less than about 1 mm disposed along a wall of the pestle.
  • the plurality of features of the vessel and/or the plurality of features of the pestle are arranged in a sawtooth pattern (FIG. 11 ).
  • the pestle may contain a handle, e.g., for facile manipulation.
  • the samples that may be used with the devices and kits described herein may be any liquid, e.g., an aqueous liquid, that contains biological particles (e.g., cells or particulate components thereof, e.g., organelles, such as nuclei).
  • the samples may contain insoluble substances, e.g., cellular debris, proteins, nucleic acids, etc. including extracellular molecules or analytes.
  • unwanted molecules or analytes in a sample containing cells may be extracellular molecules or analytes.
  • Extracellular analytes may be chemical, biological, or biochemical molecules or particles that are outside of a cell.
  • the extracellular analytes may include any kind of molecules, such as nucleic acid molecules, peptides, proteins, substrates, a sequence of nucleic acids, a sequence of amino acids, or other kinds of molecules.
  • Extracellular molecules may include extracellular nucleic acid molecules such as DNA and/or RNA or any other types of nucleic acid molecules and/or any combination thereof that are not inside a cell or cell nucleus.
  • extracellular molecules may be impurities in the sample. Additional disclosure regarding unwanted extracellular analytes is provided in U.S. Provisional Patent Application No. 63/109,972, which is incorporated here by reference in its entirety.
  • Extracellular molecules may also be referred to as free-floating molecules (e.g., free-floating nucleic acid molecules), ambient molecules (e.g., ambient nucleic acid molecules), and/or background molecules (e.g., background nucleic acid molecules).
  • Extracellular molecules may include molecules in a sample that are not inside a cell or cell nucleus which may act as impurities and may interfere with the quality of data obtained from analyzing the cells or cell nuclei of the sample. In some cases, extracellular molecules may be present without interfering with the quality of data obtained from analyzing the cells or cell nuclei of the sample.
  • the extracellular molecules may include molecules such as extracellular peptides, proteins, substrates, a sequence of amino acids, chemicals, impurities and/or any combination thereof.
  • a sample with a cell or cell nucleus may further include extracellular molecules such as proteins and/or peptides.
  • the extracellular molecules may include or be extracellular nucleic acid molecules.
  • extracellular nucleic acid molecules may include ribonucleic acid (RNA) or deoxyribonucleic acid (DNA).
  • extracellular nucleic acid may include at least one of messenger RNA (mRNA), chromosome, and genomic DNA (gDNA).
  • the extracellular nucleic acid molecules may have a size of at least about 5 base pairs (bp) or nucleotides (nt), for example, at least about 5 bp or nt, 10 bp or nt, 15 bp or nt, 20 bp or nt, 25 bp or nt, 30 bp or nt, 35 bp or nt, 40 bp or nt 50 bp or nt, 60 bp or nt, 70 bp or nt, 80 bp or nt, 90 bp or nt, 100 bp or nt, 200 bp or nt, 300 bp or nt, 400 bp or nt, 500 bp or nt, 600 bp or nt, 700 bp or nt, 800 bp or nt, 900 bp or nt, 1 kbp or knt, or larger
  • extracellular nucleic acid molecules may be equal to or smaller than about: 500 bp or nt, 400 bp or nt, 300 bp or nt, 200 bp or nt, 100 bp or nt, 50 bp or nt,40 bp or nt, 30 bp or nt, 20 bp or nt, 10 bp or nt, 5 bp or nt, or smaller, for example smaller than 50 bp or nt.
  • Extracellular analytes may have been released in the sample from a cell or cell nucleus, for example, as a result of processing, treating, and/or manipulating a sample including a cell and/or a cell nucleus (e.g., during sample preparation). Such processing may have caused cell lysis or a loss of the integrity of the cell membrane and/or the nuclear membrane. This phenomenon may occur in any kind of cell, such as any cell type listed elsewhere herein or other types of cells. In some cases, a cell type that is more fragile may be more prone to getting lysed during sample preparation. Such cell type may be more likely to release extracellular molecules in the sample.
  • the extracellular molecules may have other origins and/or causes. Recognized is a need to address a contamination (or cross-contamination) of a sample with extracellular molecules (e.g., extracellular nucleic acid molecules) and their interference with data analysis (e.g., single cell analysis such as single cell sequencing or other sample processing and analysis techniques or procedures).
  • data analysis e.g., single cell analysis such as single cell sequencing or other sample processing and analysis techniques or procedures.
  • the presence of extracellular molecules may adversely affect and/or at least to some extent compromise the precision or quality of the results of the analysis (e.g., single cell analysis and/or data clustering results).
  • the goal may be to analyze the nucleic acid molecules in the cells and/or cell nuclei (e.g., intracellular nucleic acid molecules) of the sample.
  • the method may further include clustering the data generated for the cells and/or the cell nuclei of the sample into more than one subpopulation (e.g., cluster the cell into multiple subpopulations).
  • the method may further include identifying combinations of characteristics and/or parameters (e.g., markers) that may provide important information regarding each subpopulation and/or define the subpopulation in terms of a given state or condition of the sample or the subject, for example a disease marker or a diagnosis of the subject.
  • characteristics and/or parameters e.g., markers
  • the presence of extracellular molecules such as extracellular nucleic acid molecules may interfere with such clustering and/or identification in one or more ways. This phenomenon may also be referred to as cross contamination.
  • extracellular molecules e.g., ambient or background molecules such as nucleic acid molecules
  • the data e.g., signal or sequencing reads
  • Extracellular molecules e.g., extracellular nucleic acid molecules
  • Extracellular molecules may cause artifacts and/or noise in the data, alter the number of subpopulations resulted from the cluster analysis, interfere with the data in other ways, and/or any combinations thereof. This may cause imprecision in data and may adversely affect interpretation of results and/or decision making based on such data and/or data clustering. Therefore, depending on the application, there may be a need to ascertain the composition of a sample prior to use in, for example, single cell processing, including partitioning.
  • the extracellular molecules such as nucleic acid molecules inside a sample that are external to a cell or cell nucleus may generate information, such as signals (e.g., sequence reads) during sample processing and/or analysis.
  • a sample including a cell or cell nucleus which also includes extracellular nucleic acid molecules may be subjected to processing and analysis, for example, single cell sequencing (e.g., single cell RNA sequencing).
  • the signals obtained from the extracellular nucleic acid molecules may be considered noise and may contaminate the data obtained from the intracellular nucleic acid molecules or data obtained from the nucleic acid molecules inside the cell nuclei.
  • digesting or otherwise decreasing or removing the extracellular nucleic acid molecules from the sample may enhance the quality of the single cell sequencing data and a clustering thereof.
  • reduced amounts of extracellular molecules may result in more precise and/or more informative data with reduced noise, artifacts, imprecision, and/or error. Such data may include higher quality and may result in improved interpretation of results and/or more informed decision making.
  • the elimination of extracellular molecules may reduce the time and expense of data analysis, for example, by providing cleaner data with reduced noise.
  • the devices described herein are particularly advantageous for small volumes of sample (e.g., less than 100 mI_, 90 mI_, 80 mI_, 70 mI_, 60 mI_, 50 mI_, 40 mI_, 30 mI_, 20 mI_, 10 mI_, 9 mI_, 8 mI_, 7 mI_, 6 mI_, 5 mI_, 4 mI_,
  • sample e.g., less than 100 mI_, 90 mI_, 80 mI_, 70 mI_, 60 mI_, 50 mI_, 40 mI_, 30 mI_, 20 mI_, 10 mI_, 9 mI_, 8 mI_, 7 mI_, 6 mI_, 5 mI_, 4 mI_,
  • volume of samples that contain a low number of biological particles e.g., a cell or particulate component thereof, e.g., a nucleus.
  • Biological particles in the samples may be purified using the invention before incorporation into droplets.
  • the samples may be derived from droplets, e.g., following breaking or destabilization of droplets.
  • Droplets generally refer to one liquid suspended in a second immiscible liquid and may be formed in which one or more biological particles are encapsulated within the droplet.
  • the biological particles may be suspended in any suitable buffer.
  • cells may be suspended in a suitable cell lysis buffer.
  • the cell lysis buffer may include an RNAse inhibitor.
  • the cell lysis buffer may include a surfactant (e.g., from about 0.01% to about 1.0% of the surfactant).
  • the cell lysis buffer includes 10 mM Tris-HCI (pH 7.4), 10 mM NaCI, 3 mM MgCI 2 , 0.01% IGEPAL CA-630 (octylphenoxypolyethoxyethanol), 0.2 U/mI RNase Inhibitor (e.g., enzymatic RNAse inhibitor, e.g.,
  • RNAse 0.1% BSA, 2 mM spermine, and from about 0.01% to about 1 .0% of a surfactant/detergent (e.g., TWEEN-20 (polysorbate 20) or IGEPAL CA-630
  • a surfactant/detergent e.g., TWEEN-20 (polysorbate 20) or IGEPAL CA-630
  • the lysis buffer may include, e.g., 10 mM Tris-HCI (pH 7.4), 10 mM NaCI, 3 mM MgCL, 0.01% IGEPAL CA-630 (octylphenoxypolyethoxyethanol), 0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2 mM spermine, and 0.1% TWEEN-20 (polysorbate 20). If organelles, such as nuclei, are to be purified from cells, the cells may be lysed in the lysis buffer. The nuclei may then be resuspended in an isotonic buffer for dispensing into the inlet of the vessel.
  • the isotonic buffer may include an RNAse inhibitor.
  • the isotonic buffer may include a surfactant (e.g., from about 0.01% to about 1.0% of the surfactant).
  • a suitable isotonic buffer may include, e.g., 20 mM Tris-HCI (pH 7.4), 0.25 M sucrose, 25 mM KCI, 5 mM MgCL, 0.01% IGEPAL CA-630, 0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2 mM spermine, and 0.1% TWEEN-20.
  • the sample comprising cells or the sample comprising lysed cells is subjected to a debris removal process in which a debris removal buffer is utilized.
  • the debris removal buffer comprises a debris removal agent and a reducing agent.
  • the sample comprising cells or the sample comprising lysed cells is subjected to a wash and resuspension buffer, wherein the wash and resuspension buffer comprises an optional RNase inhibitor; bovine serum albumin (BSA), which may be about 1%, 5%, or 10% final concentration; and a buffered saline such as phosphate buffered saline (PBS).
  • BSA bovine serum albumin
  • PBS buffered saline
  • the biological particles may be suspended or resuspended in a diluent.
  • the diluent may be a second liquid having a second density, e.g., that is lower than the density of the first liquid.
  • the second liquid may include iodixanol.
  • the second layer may include from about 5% to about 45% iodixanol (e.g., from about 10% to about 40%, from about 15% to about 35%, from about 20% to about 30%, from about 21 to about 29%, from about 22% to about 28%, from about 23% to about 27 %, from about 24% to about 26%, from about 24.5% to about 26.5%, e.g., about 25%.
  • the biological sample or the biological particles thereof e.g., cells or nuclei
  • a device, kit, or method e.g., lysis or purification method
  • the biological sample may be subject to multiple rounds of lysis and/or purification and used in different methods as described herein.
  • the devices and systems described herein may be used for purification of biological particles (e.g., cells or particulate components thereof, e.g., nuclei) for incorporation into droplets or particles.
  • a device for producing droplets or particles may be used in conjunction with the kits and methods described herein.
  • kits described herein may be used in conjunction with a device for producing droplets that contain the purified biological particles.
  • droplets or particles are provided by a droplet or particle source.
  • the droplets or particles may be first formed by flowing a first liquid through a channel and into a droplet or particle source region including a second liquid, i.e., the continuous phase, which may or may not be actively flowing.
  • Devices for producing droplets or particles include a droplet or particle source.
  • the droplet or particle source provides droplets or particles, e.g., for subsequent use.
  • the droplet or particle source may include a droplet or particle source region.
  • Droplets or particles may be formed by any suitable method known in the art. In general, droplet formation includes two liquid phases. The two phases may be, for example, the sample phase and an oil phase. During formation, a plurality of discrete volume droplets or particles are formed.
  • the droplets may be formed by shaking or stirring a liquid to form individual droplets, creating a suspension or an emulsion containing individual droplets, or forming the droplets through pipetting techniques, e.g., with needles, or the like.
  • the droplets may be formed made using a milli-, micro-, or nanofluidic droplet maker.
  • droplet makers include, e.g., a T-junction droplet maker, a Y-junction droplet maker, a channel-within-a-channel junction droplet maker, a cross (or “X”) junction droplet maker, a flow-focusing junction droplet maker, a micro-capillary droplet maker (e.g., co-flow or flow-focus), and a three-dimensional droplet maker.
  • the droplets may be produced using a flow-focusing device, or with emulsification systems, such as homogenization, membrane emulsification, shear cell emulsification, and fluidic emulsification.
  • Discrete liquid droplets may be encapsulated by a carrier fluid that wets the microchannel. These droplets, sometimes known as plugs, form the dispersed phase in which the reactions occur. Systems that use plugs differ from segmented-flow injection analysis in that reagents in plugs do not come into contact with the microchannel. In T junctions, the disperse phase and the continuous phase are injected from two branches of the “T”. Droplets of the disperse phase are produced as a result of the shear force and interfacial tension at the fluid-fluid interface. The phase that has lower interfacial tension with the channel wall is the continuous phase.
  • the continuous phase is injected through two outside channels and the disperse phase is injected through a central channel into a narrow orifice.
  • Other geometric designs to create droplets would be known to one of skill in the art. Methods of producing droplets are disclosed in Song et al. Angew. Chem. 45: 7336- 7356, 2006, Mazutis et al. Nat. Protoc. 8(5):870-891 , 2013, U.S. Pat. No. 9,839,911 ; U.S. Pub. Nos. 2005/0172476, 2006/0163385, and 2007/0003442, PCT Pub. Nos. WO 2009/005680 and WO 2018/009766.
  • electric fields or acoustic waves may be used to produce droplets, e.g., as described in PCT Pub. No. WO 2018/009766.
  • the droplet source region includes a shelf region that allows liquid to expand substantially in one dimension, e.g., perpendicular to the direction of flow.
  • the width of the shelf region is greater than the width of the first channel at its distal end.
  • the first channel is a channel distinct from a shelf region, e.g., the shelf region widens or widens at a steeper slope or curvature than the distal end of the first channel.
  • the first channel and shelf region are merged into a continuous flow path, e.g., one that widens linearly or non-linearly from its proximal end to its distal end; in these embodiments, the distal end of the first channel can be considered to be an arbitrary point along the merged first channel and shelf region.
  • the droplet source region includes a step region, which provides a spatial displacement and allows the liquid to expand in more than one dimension. The spatial displacement may be upward or downward or both relative to the channel.
  • Droplet source regions may also include combinations of a shelf and a step region, e.g., with the shelf region disposed between the channel and the step region. Exemplary devices of this embodiment are described in WO 2019/040637, WO 2020/139844, and WO 2020/176882, the droplet forming devices of which are hereby incorporated by reference.
  • the invention contemplates lysis and/or purification of biological particles from biological samples.
  • Biological particles include, e.g., cells or particulate components thereof, e.g., organelles, such as a nucleus or a mitochondrion) and/or macromolecular constituents thereof (e.g., components of cells (e.g., intracellular or extracellular proteins, nucleic acids, glycans, or lipids) or products of cells (e.g., secretion products)).
  • the biological particles may be provided by the devices, kits, and methods of the present invention.
  • Cellular analytes or analytes originating from biological particles (e.g., cells or nuclei), may be used and may include, without limitation, any or all molecules or substances from or produced by a cell.
  • cellular analytes may include proteins, polypeptides, peptides, saccharides, polysaccharides, lipids, nucleic acids, combinations thereof and other biomolecules.
  • a cellular analyte may include a protein, a metabolite, a metabolic byproduct, an antibody or antibody fragment, an enzyme, an antigen, a carbohydrate, a lipid, a macromolecule, or a combination thereof (e.g., proteoglycan) or other biomolecule.
  • the cellular analyte may be a nucleic acid molecule.
  • the cellular analyte may be a deoxyribonucleic acid (DNA) molecule or a ribonucleic acid (RNA) molecule.
  • the DNA molecule may be a genomic DNA molecule.
  • the cellular analyte may include coding or non-coding RNA.
  • the RNA may be messenger RNA (mRNA), ribosomal RNA (rRNA) or transfer RNA (tRNA), for example.
  • the RNA may be a transcript.
  • the RNA may be small RNA that are less than 200 nucleic acid bases in length, or large RNA that are greater than 200 nucleic acid bases in length.
  • Small RNAs may include 5.8S ribosomal RNA (rRNA), 5S rRNA, transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA) and small rDNA-derived RNA (srRNA).
  • rRNA ribosomal RNA
  • 5S rRNA transfer RNA
  • tRNA transfer RNA
  • miRNA microRNA
  • siRNA small interfering RNA
  • snoRNAs small nucleolar RNA
  • piRNA tRNA-derived small RNA
  • srRNA small rDNA-derived RNA
  • the RNA may be double-stranded RNA or single-stranded RNA.
  • the RNA may be circular RNA.
  • the analytes may be contained in a sample.
  • a sample may contain only analytes or may contain analytes in addition to one or more additional components.
  • the sample may contain biological particles.
  • biological particles may be cells, parts of cells or cell organelles, like a cell nucleus.
  • a biological particle may include a cell, without any limitation on the kind or type of cell.
  • Cells may be eukaryotic, prokaryotic or archaea. Cells may be eukaryotic cells from a cell line or cell culture sample.
  • a cell may be a mammalian cell.
  • a cell may be an animal cell.
  • a cell may be a human cell.
  • a cell may be from a cell culture.
  • a cell may be from an immortalized cell line.
  • a cell may be from a primary sample, such as a patient sample.
  • a cell may be from a frozen stock of cells (e.g., cryopreserved cells).
  • the cells may be adherent cells or suspension cells.
  • the cells may be from a tissue sample, such as a biopsy, core biopsy, needle aspirate, or fine needle aspirate.
  • the sample containing cells may come from bodily fluids, such as blood, urine or saliva.
  • the sample may be a skin sample.
  • the sample may be a cheek swab.
  • the sample may contain peripheral blood mononuclear cells (PBMCs). Samples that include parts of or organelles from cells are also encompassed by this disclosure.
  • a sample may contain a cell nucleus from a eukaryotic cell.
  • the tissue sample is about 1 mg to about 10Omg. In some aspects, the tissue sample is about 1 mg to about 90mg, about 1 mg to about 80mg, about 1 mg to about 70mg, about 1 mg to about 60mg, about 1 mg to about 50mg, about 1 mg to about 40mg, about 1 mg to about 30mg, about 1 mg to about 20mg, about 1 mg to about 10mg, about 1 mg to about 5mg, about 5mg to about 10Omg, 5mg to about 70mg, about 5mg to about 60mg, about 5mg to about 50mg, about 5mg to about 40mg, about 5mg to about 30mg, about 5mg to about 20mg, about 5mg to about 10mg, about 10mg to about 100mg, about 10mg to about 70mg, about 10mg to about 60mg, about 10mg to about 50mg, about 10mg to about 40mg, about 10mg to about 30mg, about 1
  • Cells include, for example, a plant cell, animal cell, human cell, insect-derived cells, bacteria, algae, cardiomyocytes, stem cells, neurons, primary neurons, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), hepatocytes, primary heart valve cells, primary hematopoietic cells, gastrointestinal cells, lymphocytes, T-cells, B-cells, natural killer cells, dendritic cells, hematopoietic cells, beta cells, somatic cells, germ cells, embryos (human and animal), zygotes, gametes, hepatocytes, adipocytes, and cardiomyocytes.
  • ESCs embryonic stem cells
  • iPSCs induced pluripotent stem cells
  • the tissues may comprise cells from the kidney, liver, brain, heart, small intestine, eye, skeletal muscles, spinal cord, bladder, ovaries, colon, stomach, testes, jejunum, duodenum, ileum, breast, prostate, and any one or more cancerous tissues thereof.
  • a biological particle may be obtained by using lysis reagents in order to release the contents (e.g., contents of the cell or contents containing one or more analytes (e.g., bioanalytes)) of the biological particles.
  • the lysis agents can be contacted with the biological particle suspension concurrently with, or immediately prior to the introduction of the biological sample or biological particles.
  • lysis agents include bioactive reagents, such as lysis enzymes that are used for lysis of different cell types, e.g., gram positive or negative bacteria, plants, yeast, mammalian, etc., such as lysozymes, achromopeptidase, lysostaphin, labiase, kitalase, lyticase, and a variety of other lysis enzymes available from, e.g., Sigma-Aldrich, Inc. (St Louis, MO), as well as other commercially available lysis enzymes.
  • bioactive reagents such as lysis enzymes that are used for lysis of different cell types, e.g., gram positive or negative bacteria, plants, yeast, mammalian, etc., such as lysozymes, achromopeptidase, lysostaphin, labiase, kitalase, lyticase, and a variety of other lysis enzymes available from, e.g., Sigma-Ald
  • lysis agents may additionally or alternatively be used with the biological particles (e.g., cells or particulate components thereof, e.g., nuclei) to cause the release of the biological particles’ contents during purification.
  • the biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • surfactant-based lysis solutions may be used to lyse cells, although these may be less desirable for emulsion-based systems where the surfactants can interfere with stable emulsions.
  • lysis solutions may include non-ionic surfactants such as, for example, TRITON X-100 and TWEEN 20.
  • lysis solutions may include ionic surfactants such as, for example, sarcosyl and sodium dodecyl sulfate (SDS).
  • lysis solutions are hypotonic, thereby lysing cells by osmotic shock. Electroporation, thermal, acoustic, or mechanical cellular disruption may also be used in certain cases.
  • reagents can also be used with the biological particles, including, for example, DNase and RNase inactivating agents or inhibitors, such as proteinase K, chelating agents, such as EDTA, and other reagents employed in removing or otherwise reducing negative activity or impact of different cell lysate components on subsequent processing of nucleic acids.
  • DNase and RNase inactivating agents or inhibitors such as proteinase K
  • chelating agents such as EDTA
  • reagents employed in removing or otherwise reducing negative activity or impact of different cell lysate components on subsequent processing of nucleic acids.
  • Macromolecular components e.g., bioanalytes
  • individual biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • unique identifiers e.g., barcodes
  • any given component e.g., bioanalyte
  • the ability to attribute characteristics to individual biological particles or groups of biological particles is provided by the assignment of unique identifiers specifically to an individual biological particle or groups of biological particles.
  • Unique identifiers for example, in the form of nucleic acid barcodes, can be assigned or associated with individual biological particles (e.g., cells or particulate components thereof, e.g., nuclei) or populations of biological particles (e.g., cells or particulate components thereof, e.g., nuclei), in order to tag or label the biological particle’s macromolecular components (and as a result, its characteristics) with the unique identifiers. These unique identifiers can then be used to attribute the biological particle’s components and characteristics to an individual biological particle or group of biological particles. In certain embodiments in which droplets are produced, this can be performed by forming droplets including the individual biological particle or groups of biological particles with the unique identifiers (via particles, e.g., beads), as described in the kits and methods herein.
  • individual biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • populations of biological particles e.g., cells or particulate components thereof,
  • the unique identifiers are provided in the form of oligonucleotides that comprise nucleic acid barcode sequences that may be attached to or otherwise associated with the nucleic acid contents of individual biological particle, or to other components of the biological particle, and particularly to fragments of those nucleic acids.
  • the oligonucleotides are partitioned such that as between oligonucleotides in a given droplet, the nucleic acid barcode sequences contained therein are the same, but as between different droplets, the oligonucleotides can, and do have differing barcode sequences, or at least represent a large number of different barcode sequences across all of the droplets in a given analysis.
  • nucleic acid barcode sequences can include from 6 to about 20 or more nucleotides within the sequence of the oligonucleotides. In some cases, the length of a barcode sequence may be 6, 7, 8, 9,
  • the length of a barcode sequence may be at least 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20 nucleotides or longer. In some cases, the length of a barcode sequence may be at most 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20 nucleotides or shorter. These nucleotides may be completely contiguous, i.e., in a single stretch of adjacent nucleotides, or they may be separated into two or more separate subsequences that are separated by 1 or more nucleotides.
  • separated barcode subsequences can be from about 4 to about 16 nucleotides in length.
  • the barcode subsequence may be 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16 nucleotides or longer.
  • the barcode subsequence may be at least 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16 nucleotides or longer.
  • the barcode subsequence may be at most 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16 nucleotides or shorter.
  • Analyte moieties can also include other functional sequences useful in processing of nucleic acids from biological particles contained in the sample. These sequences include, for example, targeted or random/universal amplification primer sequences for amplifying the genomic DNA from the individual biological particles within the droplets while attaching the associated barcode sequences, sequencing primers or primer recognition sites, hybridization or probing sequences, e.g., for identification of presence of the sequences or for pulling down barcoded nucleic acids, or any of a number of other potential functional sequences.
  • sequences include, for example, targeted or random/universal amplification primer sequences for amplifying the genomic DNA from the individual biological particles within the droplets while attaching the associated barcode sequences, sequencing primers or primer recognition sites, hybridization or probing sequences, e.g., for identification of presence of the sequences or for pulling down barcoded nucleic acids, or any of a number of other potential functional sequences.
  • particles e.g., beads
  • hydrogel beads e.g., beads having polyacrylamide polymer matrices
  • oligonucleotides e.g., into droplets
  • they are capable of carrying large numbers of oligonucleotide molecules and may be configured to release those oligonucleotides upon exposure to a particular stimulus, as described elsewhere herein.
  • the population of beads will provide a diverse barcode sequence library that includes at least about 1 ,000 different barcode sequences, at least about 5,000 different barcode sequences, at least about 10,000 different barcode sequences, at least about 50,000 different barcode sequences, at least about 100,000 different barcode sequences, at least about 1 ,000,000 different barcode sequences, at least about 5,000,000 different barcode sequences, or at least about 10,000,000 different barcode sequences, or more. Additionally, each bead can be provided with large numbers of oligonucleotide molecules attached.
  • the number of molecules of oligonucleotides including the barcode sequence on an individual bead can be at least about 1 ,000 oligonucleotide molecules, at least about 5,000 oligonucleotide molecules, at least about 10,000 oligonucleotide molecules, at least about 50,000 oligonucleotide molecules, at least about 100,000 oligonucleotide molecules, at least about 500,000 oligonucleotides, at least about 1 ,000,000 oligonucleotide molecules, at least about 5,000,000 oligonucleotide molecules, at least about 10,000,000 oligonucleotide molecules, at least about 50,000,000 oligonucleotide molecules, at least about 100,000,000 oligonucleotide molecules, and in some cases at least about 1 billion oligonucleotide molecules, or more.
  • a population of beads can also include a diverse barcode library that includes at least about 1 ,000 different barcode sequences, at least about 5,000 different barcode sequences, at least about 10,000 different barcode sequences, at least at least about 50,000 different barcode sequences, at least about 100,000 different barcode sequences, at least about 1 ,000,000 different barcode sequences, at least about 5,000,000 different barcode sequences, or at least about 10,000,000 different barcode sequences.
  • the population can include at least about 1 ,000 oligonucleotide molecules, at least about 5,000 oligonucleotide molecules, at least about 10,000 oligonucleotide molecules, at least about 50,000 oligonucleotide molecules, at least about 100,000 oligonucleotide molecules, at least about 500,000 oligonucleotides, at least about 1 ,000,000 oligonucleotide molecules, at least about 5,000,000 oligonucleotide molecules, at least about 10,000,000 oligonucleotide molecules, at least about 50,000,000 oligonucleotide molecules, at least about 100,000,000 oligonucleotide molecules, and in some cases at least about 1 billion oligonucleotide molecules.
  • the sample may be desirable to incorporate multiple different barcodes within a sample, either attached to a single or multiple particles, e.g., beads, within the sample.
  • mixed, but known barcode sequences set may provide greater assurance of identification in the subsequent processing, for example, by providing a stronger address or attribution of the barcodes to a given sample or portion thereof, as a duplicate or independent confirmation of the output from a given sample.
  • Oligonucleotides may be releasable from the particles (e.g., beads) upon the application of a particular stimulus.
  • the stimulus may be a photo-stimulus, e.g., through cleavage of a photo-labile linkage that releases the oligonucleotides.
  • a thermal stimulus may be used, where increase in temperature of the particle, e.g., bead, environment will result in cleavage of a linkage or other release of the oligonucleotides form the particles, e.g., beads.
  • a chemical stimulus is used that cleaves a linkage of the oligonucleotides to the beads, or otherwise results in release of the oligonucleotides from the particles, e.g., beads.
  • such compositions include the polyacrylamide matrices described above for encapsulation of biological particles and may be degraded for release of the attached oligonucleotides through exposure to a reducing agent, such as dithiothreitol (DTT).
  • DTT dithiothreitol
  • the samples described herein may contain either one or more biological particles (e.g., cells or particulate components thereof, e.g., nuclei), either one or more barcode carrying particles, e.g., beads, or both at least a biological particle and at least a barcode carrying particle, e.g., bead.
  • biological particles e.g., cells or particulate components thereof, e.g., nuclei
  • barcode carrying particles e.g., beads
  • at least a biological particle and at least a barcode carrying particle e.g., bead.
  • the present methods can be applied to OCT embedded tissues, and applicant data (not presented) indicates that nuclei isolated from OCT embedded tissue are viable for downstream sample processing after isolation, and further yield strong complex data.
  • the methods described herein have yielded success in isolating viable nuclei from immunological cells; neuronal cells (brain tissue); and cancerous tissue samples, such as tumors of the kidney, breast bowel, colon, rectum, lung, skin, ovary, pancrease, and prostate.
  • Incompatible samples are calcified tissues such as bone, plant tissues, chitinous insect tissues, and fixed tissues (such as FFPE or PFA samples).
  • the invention provides methods for purifying biological particles (e.g., cells or particulate components thereof, e.g., organelles, such as nuclei), e.g., from a biological sample (e.g., a tissue sample, e.g., a frozen tissue sample).
  • a biological sample e.g., a tissue sample, e.g., a frozen tissue sample.
  • the biological sample may be lysed, e.g., via a method as described herein, via a lysis buffer, sonication, mechanical lysis, or a combination thereof.
  • the methods described herein may be used to purify the biological particles, e.g., by at least 50% (e.g., by at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or more) relative to the starting mixture.
  • Biological particles are in general purified by providing a kit of the invention and providing a liquid mixture that includes biological particles to the inlet of the vessel.
  • the density of the liquid mixture is less than the density of the liquid layer in the vessel.
  • the thixotropic layer maintains the density gradient of the first liquid between the outlet and the thixotropic layer.
  • the method typically includes centrifuging the vessel.
  • the thixotropic layer separates the first layer and the liquid mixture and allows passage of the biological particles through the thixotropic layer to the first layer during centrifugation.
  • Various cellular debris and full cells may remain in the top layer above the thixotropic layer, whereas particulate components, such as organelles (e.g., nuclei), may pellet at the bottom of the vessel.
  • the method may further include removing a supernatant liquid after centrifugation, e.g., via decanting or discarding the supernatant.
  • the vessel may be inserted in an outer vessel to collect a flow through liquid.
  • the method may include opening a tip of the vessel to create the outlet, such that liquid can flow through the outlet.
  • the method may further include eluting the biological particles. Eluting may include centrifuging the vessel such that the biological particles exit the vessel via the outlet and are collected in the outer vessel.
  • the method may further include washing the biological particles.
  • the method may further include resuspending the biological particles, e.g., in a suitable storage buffer, such as an isotonic buffer, e.g., before or after eluting.
  • the invention features a method of purifying biological particles with a centrifuge tube.
  • the centrifuge tube contains a liquid composed of cell culture medium and a predetermined density of, e.g., from about 10% to about 50% iodixanol, e.g., from about 15% to about 45%, from about 20% to about 35%, from about 22% to about 32%, or from about 24% to about 30%, e.g., from about 24% to about 30% iodixanol, or a density of, e.g., from about 1 .11 g/mL to about 1.2 g/mL (e.g., from about 1.146 g/ml_ to about 1.175, e.g., about 1.1107 g/mL, 1 .117 g/mL, 1.127 g/mL, 1.136 g/mL, 1.146 g/mL, 1.156 g/mL, 1.165 g/mL, or 1 .175
  • the centrifuge tube may be centrifuged with the liquid having a suspension of biological particles (e.g., cells or nuclei).
  • biological particles e.g., cells or nuclei.
  • the density of the liquid allows the biological particles to pellet at the bottom of the centrifuge tube, and the debris remains in solution due to the small size (FIG. 2).
  • Centrifugation can be performed at a single speed or at multiple speeds.
  • a liquid mixture may be centrifuged at a first speed (e.g., from about 150g to about 300g, e.g., for about 5 to about 10 minutes) and then centrifuged at a second speed (e.g., higher than the first, e.g., from about 500g to about 10OOg, e.g., for about 5 to about 10 minutes, e.g., about 10 minutes).
  • a first speed e.g., from about 150g to about 300g, e.g., for about 5 to about 10 minutes
  • a second speed e.g., higher than the first, e.g., from about 500g to about 10OOg, e.g., for about 5 to about 10 minutes, e.g., about 10 minutes.
  • the method may further include removing a supernatant liquid after centrifugation, e.g., via decanting or discarding the supernatant.
  • the method may further include washing the biological particles.
  • the method may further include resuspending the biological particles, e.g., in a suitable storage buffer, such as an isotonic buffer, e.g., before or after eluting.
  • Suitable storage buffers include, for example, phosphate buffered saline, or a buffer containing, e.g., 20 mM Tris-HCI (pH 7.4), 0.25 M sucrose, 25 mM KCI, 5 mM MgCI 2 , 0.01% IGEPAL CA-630,0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2mM spermine, and 0.1% TWEEN-20 (polysorbate 20).
  • phosphate buffered saline or a buffer containing, e.g., 20 mM Tris-HCI (pH 7.4), 0.25 M sucrose, 25 mM KCI, 5 mM MgCI 2 , 0.01% IGEPAL CA-630,0.2 U/mI SUPERase In RNase Inhibitor, 0.1% BSA, 2mM spermine, and 0.1% TWEEN-20 (polysorbate 20).
  • a first centrifugation step is performed in which all contents of the sample are pelleted. Following the first centrifugation, the supernatant may be removed, e.g., via decanting or discarding. A cell culture medium may then be added to the pellet.
  • the cell culture medium may have a predetermined density of, e.g., from about 10% to about 50% iodixanol, e.g., from about 15% to about 45%, from about 20% to about 35%, from about 22% to about 32%, or from about 24% to about 30%, e.g., from about 24% to about 30% iodixanol, or a density of, e.g., from about 1.11 g/mL to about 1.2 g/ml_, e.g., from about 1.146 g/mL to about 1.175, e.g., about 1.1107 g/mL, 1.117 g/mL, 1.127 g/mL,
  • the methods described herein include purifying a second subset of biological particles using a kit as described herein, e.g., containing a device with an inlet, an outlet, and a filter positioned in the device.
  • the kit further includes a vessel in which the device fits.
  • the method includes providing the kit, providing a liquid mixture with biological particles to the inlet of the device; and centrifuging the device in the vessel. A first subset of the biological particles is trapped by the filter, and a second subset of the biological particles exits the outlet and is collected in the vessel.
  • the vessel includes a medium having a density of greater than 1.0 g/m, and the second subset of biological particles is collected in the medium, e.g., pelleted during centrifugation.
  • the methods of purification described herein allow a user to produce a population of biological particles having desired characteristics.
  • purification generates populations of biological particles that include a suitable fraction of usable (e.g., viable) cells or particulate components thereof, e.g., organelles, e.g., nuclei (e.g., from 50% to 100%, from 60% to 100%, from 70% to 100%, from 80% to 100%, from 90% to 100%, or from 95% to 100% of biological particles).
  • a suitable fraction of usable (e.g., viable) cells or particulate components thereof e.g., organelles, e.g., nuclei (e.g., from 50% to 100%, from 60% to 100%, from 70% to 100%, from 80% to 100%, from 90% to 100%, or from 95% to 100% of biological particles).
  • the purification generates at least 10% e.g., at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%, or 100%, of the biological particles are usable for a desired purpose.
  • the methods of purification may be performed in manner that does not disturb the integrity of the cell, alter the characteristics (e.g., gene expression), activate, deactivate, differentiate, or reduce viability of the cell.
  • the relative expression level of each gene varies by less than 50%, less than 40%, less than 30 %, less than 20%, less than 10%, less than 5%, less than 2%, or less than 1%. In some embodiments, the relative expression level of each gene of the cell remains substantially constant.
  • the methods do not activate or deactivate the cell.
  • the purification may avoid mechanically disrupting a cell, which disruption would trigger a signaling cascade that activates or deactivates the cell (e.g., immune cell, such as a T cell or B cell).
  • the methods of purification do not damage or kill the biological particles (e.g., cells or particulate components thereof, e.g., nuclei), e.g., causing leakage of the contents therein.
  • the methods of purification do not trigger apoptosis or necrosis.
  • the methods described herein may be used to purify biological particles (e.g., cells or particulate components thereof, e.g., nuclei), e.g., to produce populations of biological particles of uniform and predictable sizes with high throughput.
  • the methods may be employed to purify biological particles for subsequent use, such as incorporation into droplets as microscale chemical reactors, where the volumes of the chemical reactants are small ( ⁇ pl_s).
  • the invention features a method of lysing biological particles with a device with one or more sharp features.
  • the device includes a flow path having an inlet and an outlet and at least one sharp feature disposed in the flow path.
  • the method includes providing the device and flowing a liquid mixture containing the biological particles through the flow path (e.g., via the inlet).
  • the biological particles are lysed upon interaction with the sharp feature, and at least a portion of the biological particles or the contents thereof exit the flow path via the outlet.
  • the method may further include washing the biological particles in the flow path, e.g., one or more times, e.g., with a suitable wash buffer (e.g., phosphate buffered saline).
  • a suitable wash buffer e.g., phosphate buffered saline
  • the method includes providing magnetic particles to the liquid mixture or to the flow path (FIG. 4).
  • the magnetic particles e.g., beads
  • the magnetic particles may be configured to bind to and/or capture biological material, such as background (e.g., cytoplasmic) RNA after cell rupture.
  • the magnetic particles may also increase the efficiency of lysis of the biological particles.
  • the magnetic particles may be used to separate out the biological material attached to the magnetic particles (e.g., by pelleting the magnetic particles) or using a magnet to selectively remove or move the magnetic particles with the biological particles attached thereto.
  • the invention features a method of lysing biological particles with a device with one or more sharp features that is employed with a vessel.
  • the method includes placing the device in the vessel, e.g., a centrifuge tube.
  • the method further includes providing a liquid mixture including the biological particles to the inlet of the device and centrifuging the vessel.
  • the at least one feature lyses the biological particles, and at least a portion of the biological particles or the contents thereof exit the flow path via the outlet and are collected in the vessel.
  • desired biological particles e.g., nuclei
  • undesired biological particles are collected in the vessel.
  • different biological materials preferentially exit the outlet of the flow path at different times, thereby allowing separation.
  • desired biological particles such as nuclei
  • undesired biological materials such as cellular debris, background (e.g., cytoplasmic) RNA, or other ruptured cellular components
  • undesired biological materials such as cellular debris, background (e.g., cytoplasmic) RNA, or other ruptured cellular components
  • desired biological particles such as nuclei
  • the desired particles can be washed one or more times to remove excess undesired particles.
  • the methods of lysis described herein employ a device with a filter, e.g., positioned in the flow path at or upstream of the outlet and configured to trap particles of a predetermined size.
  • the filter may function, e.g., as a size-based filter in the flow path or as a series of obstacles.
  • the filter may trap desired biological particles.
  • the filter may trap undesired biological material.
  • the filter may also be employed upstream of the sharp features, e.g., to remove large debris (FIGS. 4 and 10).
  • the methods for lysis of biological particles include using a kit as described herein containing a device (e.g., having an inlet and an outlet and layer with a flow path having at least one feature with a corner radius of less than about 1 mm disposed in the flow path) and a vessel to house the device.
  • the method includes providing the kit, providing a liquid mixture with biological particles to the inlet of the device; and centrifuging the device in the vessel.
  • the at least one feature lyses the biological particles, and at least a portion of the contents of the biological particle exits the flow path via the outlet and is collected in the vessel.
  • the vessel includes a medium having a density of greater than 1.0 g/m, and the contents of the biological particles are collected in the medium, e.g., pelleted during centrifugation.
  • the device further includes a filter disposed in the device, and the filter traps biological particles of a predetermined size in the filter, e.g., prior to or following lysis.
  • the methods of lysis include employing a kit with a vessel and a pestle, e.g., each having one or more features having a corner radius of less than about 1 mm disposed along a wall of the vessel and/or the pestle.
  • the method includes providing the kit; providing a liquid mixture containing biological particles in the vessel; and rotating the pestle (e.g., one or more times) in the vessel.
  • the features of the vessel and/or the pestle lyse the biological particles (FIG. 11).
  • the methods of lysis described herein allow a user to perform lysis in the absence of lysis reagents, such as surfactants. Additionally, the methods of lysis may be performed in the presence of amounts of lysis agents that are too low to cause lysis on their own.
  • the methods of lysis may be performed in a manner that does not disturb the integrity of certain contents of the biological particle after lysis (e.g., a cellular component, such as a nucleus), alter the characteristics (e.g., gene expression), activate, deactivate, differentiate, or reduce viability of certain contents of the biological particle.
  • a cellular component such as a nucleus
  • the relative expression level of each gene varies by less than 50%, less than 40%, less than 30 %, less than 20%, less than 10%, less than 5%, less than 2%, or less than 1% in a cellular component (e.g., a nucleus or mitochondrion).
  • the relative expression level of each gene of the cellular component remains substantially constant.
  • the methods do not activate or deactivate the biological particle.
  • the lysis may avoid mechanically disrupting a nucleus, which disruption would trigger a signaling cascade that activates or deactivates the nucleus.
  • the methods of lysis do not damage or kill the biological particles (e.g., nuclei), e.g., causing leakage of the contents therein.
  • the methods of lysis and/or purification as described herein may be used to produce biological particles for downstream methods or applications.
  • a variety of applications require the evaluation of the presence and quantification of different biological particle or organism types within a population of biological particles, including, for example, microbiome analysis and characterization, environmental testing, food safety testing, epidemiological analysis, e.g., in tracing contamination or the like.
  • Devices, systems, compositions, and methods of the present disclosure may be used for various applications, such as, for example, processing a single analyte (e.g., bioanalytes, e.g., RNA, DNA, or protein) or multiple analytes (e.g., bioanalytes, e.g., DNA and RNA, DNA and protein, RNA and protein, or RNA, DNA and protein) from a single cell or nucleus.
  • a single analyte e.g., bioanalytes, e.g., RNA, DNA, or protein
  • multiple analytes e.g., bioanalytes, e.g., DNA and RNA, DNA and protein, RNA and protein, or RNA, DNA and protein
  • a biological particle e.g., a cell, a nucleus, or virus
  • one or more analytes e.g., bioanalytes
  • the multiple analytes may be from the single cell or nucleus.
  • This process may enable, for example, proteomic, transcriptomic, and/or genomic analysis of the cell/nucleus or population thereof (e.g., simultaneous proteomic, transcriptomic, and/or genomic analysis of the cell/nucleus or population thereof).
  • Methods of modifying analytes include providing a plurality of particles (e.g., beads) in a liquid carrier (e.g., an aqueous carrier); providing a sample containing an analyte (e.g., as part of a cell, a nucleus or component or product thereof) in a sample liquid; and using the device to combine the liquids and form an analyte droplet containing one or more particles and one or more analytes (e.g., as part of one or more cells, nuclei, or components or products thereof).
  • a liquid carrier e.g., an aqueous carrier
  • an analyte e.g., as part of a cell, a nucleus or component or product thereof
  • Such sequestration of one or more particles with analyte (e.g., bioanalyte associated with a cell or a nucleus) in a droplet enables labeling of discrete portions of large, heterologous samples (e.g., single cells or nuclei within a heterologous population).
  • analyte e.g., bioanalyte associated with a cell or a nucleus
  • droplets or particles can be subsequently sorted or combined (e.g., by breaking an emulsion), and the resulting liquid can be analyzed to determine a variety of properties associated with each of numerous single cells or nuclei.
  • Another embodiment provides methods of single-cell (or single-nucleus) nucleic acid sequencing, in which a heterologous population of cells/nuclei can be characterized by their individual gene expression, e.g., relative to other cells/nuclei of the population.
  • Methods of barcoding cells/nuclei discussed above and known in the art can be part of the methods of single-cell (or single nucleus) nucleic acid sequencing provided herein. After barcoding, nucleic acid transcripts that have been barcoded are sequenced, and sequences can be processed, analyzed, and stored according to known methods. In some embodiments, these methods enable the generation of a genome library containing gene expression data for any single cell or nucleus within a heterologous population.
  • the present disclosure provides an alternative method for removing or depleting unwanted components (e.g., dead cells or extracellular molecules) from a sample with biological particles.
  • the method includes providing a sample with biological particles and unwanted components originating from biological particles (e.g., live or dead cells).
  • biological particles are live (or intact) cells or intact nuclei.
  • the biological particles are live (or intact) cells or intact nuclei.
  • the unwanted components include one or more of dead or dying cells, non-intact nuclei, extracellular analytes or molecules, and other debris.
  • the method includes magnetically labelling unwanted components (e.g., dead cells) and/or magnetically capturing or trapping unwanted components (e.g., extracellular molecules, such as background RNA) in the sample to provide a suspension (e.g., an aqueous suspension or liquid) with unwanted components that are magnetically labelled and biological particles (e.g., live cells or intact nuclei) that are un-labelled, i.e. , not magnetically labelled.
  • a magnetic particle configured to bind or trap such molecules may be used.
  • the method includes providing a device for separation that includes a flow path with an inlet and an outlet (and optionally, a vessel) and a magnetic source disposed to exert a magnetic field on the particles in the flow path or on the magnetic particles after they exit the flow path.
  • the method further includes flowing the suspension into the flow path, e.g., via the inlet.
  • the device is subjected to conditions that allow the unwanted components that are magnetically labelled to be immobilized at a location in the sample, e.g., via a magnetic source.
  • the present disclosure is drawn to methods of isolating nuclei from a cell, the methods comprising incubating mammalian cells in an isotonic buffer and passing a composition comprising the mammalian cells through a filter, wherein the passed-through composition comprises nuclei separated from cells.
  • the composition comprising the nuclei are further purified to remove cellular debris.
  • Wash and Resuspension Buffer optionally about 50-500 mI Wash and Resuspension Buffer, which may depend on expected recovery for input tissue type and mass.
  • Gently mix optionally with a pipette.
  • Vortex nuclei optionally for about 3 sec at about 3,200 rpm or max speed immediately prior to counting to ensure accurate nuclei count. Pulse spin the tube after vortexing to collect liquid at bottom of tube. Do not pulse spin the tube for more than 1 second to ensure that nuclei do not pellet at the bottom of the tube.
  • T. Determine nuclei concentration, optionally using AOPI or Ethidium Homodimer-1 fluorescent staining dyes and dilute if necessary for target nuclei load.
  • U. Vortex nuclei, optionally for about 3 sec at about 3,200 rpm or max speed. Pulse spin the tube after vortexing to collect liquid at bottom of tube. Do not pulse spin the tube for more than 1 second to ensure that nuclei do not pellet at the bottom of the tube.

Abstract

L'invention concerne des dispositifs, des kits et leurs procédés d'utilisation pour la lyse et/ou la purification de particules biologiques, par exemple, des noyaux. Une ou plusieurs couches thixotropiques peuvent être utilisées dans un récipient pour purifier des particules biologiques. Un dispositif muni d'éléments tranchants peut être utilisé pour lyser des particules biologiques ou le contenu de celles-ci.
PCT/US2022/037918 2021-07-21 2022-07-21 Procédés, dispositifs et kits pour la purification et la lyse de particules biologiques WO2023004068A2 (fr)

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