The present disclosure relates generally to the field of immunology, and particularly relates to methods for the identification and/or characterization of target specific antigen-binding molecules (e.g., antibodies) produced by immune cells within biological samples using approaches involving barcode enabled antigen mapping.
in situ in situ analysis involving preparation and treatment (e.g., de-crosslinking) of biological samples. Preparation of biological samples comprising nucleic acid analytes and protein analytes for detection are provided. Methods, in which the sample with bound probes is contacted with a buffer at a temperature above 80°C, improve the detection of optical signals associated with analytes in a fixed biological sample.
Provided herein are methods, kits, systems, and compositions for spatial analysis using one or more substrates (e.g., slides), wherein one of the substrates can have a spatial array. The methods disclosed herein include arrays having releasable capture probes that can interact with analytes or analyte derivatives and provide abundance and/or location of an analyte in a biological sample.
Provided herein are methods, compositions, systems, and kits for improved biological sample processing and single particle analysis that can involve cross-linking a particle comprising a lipid membrane and a reporter oligonucleotide to form a barcoded particle.
Modified polymerases capable of incorporating modified nucleotides are provided. In some aspects, the modified polymerases at least 80% identical to SEQ ID NO: 3 and comprising the following amino acid mutations: an L436 mutation selected from L436Y, L436S, and L436T; a Y437 mutation selected from Y437A and Y437G; and at least one of: a D165A mutation and a E167A mutation. In some aspects, the modified polymerases are used in a sequencing reaction, such as an in situ sequencing reaction.
The present disclosure relates to methods and compositions for generating amplification products associated with analytes present in a biological sample. The methods and compositions provided herein allow for efficient generation of rolling circle (RCA) products generated in a biological sample and sensitive detection of analytes. The methods comprise performing RCA in a cell or tissue sample using a polymerase, a plurality of primers, and a circular nucleic acid as a template, wherein the circular nucleic acid comprises two or more barcode sequences, and wherein the plurality of primers comprise sequences complementary to at least two different barcode sequences; and detecting the at least two different barcode sequences or complements thereof in the generated RCA product in the cell or tissue sample. The method may be carried out with a first reaction mixture comprising a polymerase with inhibited activity and a plurality of primers, and a second reaction mixture and allowing the polymerase to extend at least one primer of the plurality of primers using the circular nucleic acid as a template, thereby generating a RCA product. The circularizable probe may be ligated to produce a circular probe. The second reaction mixture may comprise at least 10% of a crowding agent and a catalytic cofactor of the polymerase. The composition may be a system with a circularizable probe comprising two or more barcode sequences; and a plurality of primers comprising sequences complementary to at least two different barcode sequences of the two or more barcode sequences, and optionally a polymerase, a ligase, and a plurality of detectably labeled probes for binding to the at least two different barcode sequences or complements thereof.
The present disclosure features methods, compositions, and kits for spatially determining the location of chromosomal conformation interactions in a biological sample.
C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/683 - Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
10.
Systems and methods for transfer of reagents between droplets
The disclosure provides systems and methods for droplet processing. For example, a method can include providing a first droplet and a second droplet. In some cases, the first droplet may have a first concentration of a reagent and the second droplet may have a second concentration of the reagent. The second droplet may comprise a bead or a biological particle. The method can also include subjecting the first droplet and the second droplet to conditions sufficient to transfer the reagent from the first droplet to the second droplet, thereby decreasing the first concentration in the first droplet and increasing the second concentration in the second droplet.
The present disclosure relates to an imaging system including: an objective having an optical axis defining a z-direction; an autofocus illumination module arranged to project, via the objective, a reference beam onto a reflective interface positioned in the field of view of the objective; and an image sensor arranged to image, via the objective, a reflection of the reference beam from the reflective interface. The autofocus illumination module is arranged so that the value of a parameter derivable from an object profile of the reference beam at the objective focal plane is an inflection value in the context of values of the parameter derivable from object profiles of the reference beam at planes corresponding to z-positions either side of the objective focal plane.
Disclosed herein is an assembly for an imaging system. The assembly comprises a base plate comprising a first end, a second end, an upper surface, and a lower surface. The assembly further comprises a first mount removably couplable to the base plate, and an alignment structure coupled to the first mount via one or more first couplings. The assembly further comprises a first optical component contacting the alignment structure to define a first set orientation of the first optical component relative to the first mount, the first optical component being coupled to the first mount in the first set orientation. The assembly further comprises a second optical component coupled to the base plate. When the first mount is removably coupled to the base plate with the first optical component in the first set orientation, the first optical component is aligned relative to the second optical component.
The present disclosure is directed to image analysis techniques for a sample, and methods and systems for correcting sample drift. In particular, a method for an imaging system is provided which comprises obtaining at least one reference image of a sample; after obtaining the at least one reference image, moving one of an objective and the sample relative to the other in an XY plane; obtaining a first image of the sample after the moving of the objective relative to the sample; and determining an offset by comparing contrast features in the first image with contrast features in the at least one reference image.
A system for precise and repeatable positioning of a cassette, e.g., for fluorescence imaging of a sample disposed on a substrate, includes a moveable stage configured for motion in an X-direction and Y-direction and a chuck disposed on the moveable stage. The chuck is configured to receive a substrate secured within the cassette, and the chuck has a first side, a second side opposite the first side, and a top surface. The chuck includes at least one magnetic component disposed in or on the chuck. The at least one magnetic component in the chuck is configured to magnetically couple to at least one magnetic component in the cassette when the cassette is positioned on the chuck.
Modified nucleotide molecules including a polyethylene glycol monophosphate linker, and methods, systems, and kits for sequencing a template nucleic acid molecule using the modified nucleotide molecules are provided. In some aspects, the modified nucleotide molecules are used in a sequencing reaction, such as an in situ sequencing reaction.
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C07H 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
A system includes a removable lid having first and second ends, top and bottom surfaces, a pivot axis at the first end, an inlet, and an outlet. The system includes a movable stage having a pedestal configured to receive a cassette. The pedestal includes at least one magnetic component configured to magnetically couple with magnetic component(s) in the cassette when the cassette is positioned on the pedestal. The stage moves the substrate between an uncoupled configuration and a coupled configuration with the removable lid. In the uncoupled configuration, the second end of the removable lid is positioned lower than the first end. In the coupled configuration, a top surface of the substrate contacts the removable lid, thereby pivoting the removable lid about the pivot axis, and horizontally aligning the removable lid with respect to the substrate, thereby forming a flow cell between the removable lid and the substrate.
This disclosure relates to a fluorescence imaging apparatus including a tube lens and an objective. The objective has an objective numerical aperture of at least 0.9 and a field of view (FOV) having an area of about 1.0 mm2to about 3.0 mm2. The objective is configured to direct emission light from its focal plane to the tube lens which is configured to focus the emission light to an image plane. Within the FOV, the objective has an effective NA profile extending radially from the center of the FOV to an outer edge of the FOV. The effective NA profile is no more than 10% below the objective NA.
Provided herein are methods for cellular analysis. A method for cellular analysis may comprise (a) providing a cell comprising a construct comprising a perturbative element, wherein the construct comprises a plurality of discrete barcode sequences that collectively identify the perturbative element; (b) contacting the cell with a plurality of discrete probes, wherein each discrete probe of the plurality of discrete probes associates with a discrete barcode sequence of the plurality of discrete barcode sequences within the cell; (c) detecting sequences of the plurality of discrete probes or derivatives thereof, thereby identifying each discrete barcode sequence of the plurality of discrete barcode sequences; and (d) using each discrete barcode sequence of the plurality of discrete barcode sequences, detected in (c), to associate the perturbative element with a genetic characteristic or phenotype of the cell.
An optofluidic instrument comprising an imaging station configured to position a sample device of a plurality of sample devices for imaging with an imaging system, a fluidics station configured to position at least one sample device of the plurality of sample devices such that the at least one sample device is capable of receiving at least one reagent from the fluidics system, and a sample handling apparatus comprising a first arm and a second arm, wherein the first and second arms are configured to engage with and lift a sample device.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Reagents, assays, enzymes, labeled and unlabeled nucleic
acids; antibodies for in vitro screening and labeling of
nucleic acids and proteins within tissue samples; buffer
solutions for scientific and medical research purposes; kits
comprised of reagents for biological analysis for medical
research and scientific research purposes; kits comprised of
reagents and single-use laboratory bottles and laboratory
pipette tips for scientific and medical research purposes;
chemical, biochemical and biological preparations for
scientific and medical research purposes; combinations of
multiple biochemical reagents commonly known as probes, each
targeted to one or more biological analytes for detection of
those biological analytes for scientific and medical
research purposes. Laboratory equipment, namely, instruments for detection of
biological molecules in tissue samples, visualization of
cells, and data analysis for scientific and medical research
purposes, namely, in situ analyzers; recorded and
downloadable computer software for the operation and control
of scientific and medical research instruments; recorded and
downloadable computer software for processing, qualifying,
quantifying, imaging, analysis or storage of medical and
scientific research data and results regarding the spatial
location or quantities of biological molecules in tissue
samples; kits comprised of reagents for scientific and
medical research purposes.
A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
The present disclosure relates in some aspects to methods and compositions for multi-functional matrix formation. In some embodiments, the multi-functional matrix is formed using a multi-arm monomer or polymer comprising a plurality of arms converging at a central branching point, each arm comprising a functional group RA, and (ii) a second monomer or polymer comprising at least two functional groups RB and a pendant tethering moiety RT.
The assembly comprises a substrate configured to receive a sample, a gasket and a cover. The gasket has an upper surface and a lower surface defining a first thickness therebetween, a void having a first cutout at a first end of the void and a second cutout at a second end of the void opposite the first end, a cover support extending into the void. The cover support has a second thickness that is less than the first thickness. The cover is configured to be positioned within the void and supported by the cover support such that, when the cover is positioned within the void, a gasket inlet is defined by the first cutout and the cover and a gasket outlet is defined by the second cutout and the cover to thereby define a closed flow cell between the substrate, gasket and cover.
The present disclosure relates in some aspects to methods for analyzing a target nucleic acid in a biological sample. In some aspects, provided herein are methods and compositions for detecting a region of interest in a target nucleic acid.
e.ge.g., a biological sample, with an imaging instrument. A first z-stack of images of a sample is captured by moving an objective of the imaging instrument relative to the sample. Each image of the first z-stack of images has a z- index within the z-stack and a first field of view. A density metric of the first z-stack of images is determined. The density metric corresponds to a point density of one or more target molecule in the first field of view. The density metric is compared with a threshold. A second z-stack is captured, based on the comparison of the metric with the threshold, by moving the objective of the imaging instrument relative to the sample. The second z-stack comprises at least one additional image of the sample within the first field of view, and is interleaved with the first z-stack.
A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
Image analysis for samples is provided. A z-stack of images of a biological sample is received. The z-stack of images corresponds to a first field of view. The first field of view comprises a plurality of patches. A fused image is generated based on the z-stack of images. The fused image is segmented to determine a first set of instances. At least one image in the z-stack of images is segmented to determine a second set of instances. A subset of the second set of instances is selected. Each instance of the subset is at least partially nonoverlapping with an instance of the first set of instances. A composite set of instances is generated based on the subset and the first set.
The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
This disclosure relates to an imaging system. The imaging system includes: an illumination dichroic mirror; a light source configured to generate illumination light and direct the illumination light to the illumination dichroic mirror. The illumination dichroic mirror is configured to direct at least a portion of the illumination light from the light source to an objective. The objective disposed to direct the illumination light to a sample positioned in the field of view of the objective. The imaging also includes an autofocus system including an autofocus light source configured to generate reference light; and an image sensor configured to receive, via the objective, a reflection of the reference light from a reflective interface in the field of view of the objective. The autofocus system is configured to direct the reference light from the autofocus light source to the illumination dichroic mirror such that the reference light is incident on the illumination dichroic mirror parallel to the illumination light, and the illumination dichroic mirror is further configured to direct at least a portion of the reference light to the objective.
The present disclosure relates in some aspects to methods and systems for analyzing a biological sample comprising contacting the biological sample with a nucleic acid probe non-covalently associated with a monomethine cyanine dye or salt thereof. In some aspects, a signal associated with the monomethine cyanine dye or salt thereof is detected to determine the location of a target analyte in the biological sample.
The present disclosure relates in some aspects to methods, compositions, and kits for using nucleotides or nucleotide analogues with modifiable fluorophores to perform nucleic acid sequencing on a template nucleic acid in a biological sample, for example in a cell or a tissue sample. In some aspects, after detecting a fluorescent intensity of a nucleotide, said nucleotide is modified to become non-fluorescent, and fluorescence of other non-modified fluorescent or non-fluorescent nucleotides can be detected. In some aspects, after detecting a fluorescent intensity of a non-modified fluorescent first nucleotide, a non-fluorescent second nucleotide is modified to become fluorescent, and fluorescence of second nucleotide can be detected. Provided herein are methods that improve sensitivity and optical resolution when performing nucleic acid sequencing reaction.
Systems, compositions, methods, and kits for spatial analysis of whole genome DNA, including targeted genomic DNA sequences, are provided. The technology is related to combining genomic DNA sequence analysis with spatial information linking the whole genome and/or targeted genomic DNA sequences to their spatial positions in single cells within biological samples. The spatial analysis of genomic DNA can be used to determine the locations of DNA sequences of interest are present anywhere in an organism's entire genome (whole genome sequence) and to identify locations of any genetic mutations, such as mutations linked to diseases and disorders.
The present disclosure relates to methods for analyzing a biological sample, comprising contacting the biological sample with labeling agents for detecting a panel of analytes in the biological sample and stripping one or more reagents by washing the biological sample in a buffer between detection of any two analytes. Provided herein are unlabeled blocking oligonucleotides to improve analyte detection.
The present disclosure relates in some aspects to methods and compositions for selectively reducing the efficiency of signal generation from one or more analytes in a biological sample. In some aspects, the methods can improve sample analysis by reducing crowding of optical signals and/or reducing sequencing reads from highly expressed analytes, such as RNA transcripts.
Disclosed herein, are compositions, methods, and kits comprising engineered reverse transcription enzymes that exhibit several desired properties such as thermal stability, processive reverse transcription, non-templated base addition, and template switching ability. The engineered reverse transcription enzymes described herein demonstrate unexpectedly higher resistance to cell lysate inhibition, greater ability to capture full-length mRNA transcripts, and demonstrate improved results in small reaction volumes as compared to other engineered reverse transcription enzymes.
The present disclosure provides methods, systems, and kits for processing or analyzing a sample. Processing a sample may comprise hybridizing a probe molecule to a binding region of a nucleic acid molecule, barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A target nucleic acid molecule in the present disclosure may comprise a CRISPR guide nucleic acid molecule or other molecule used with gene editing. Processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent binding regions of a nucleic acid molecule, linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.
In some aspects disclosed herein are methods and compositions for detecting analytes such as a plurality of nucleic acid molecules in a biological sample, said method comprising generating and analyzing a first detectable signal and a second detectable signal corresponding to a first target sequence and a second target sequence, respectively. The first and second target sequences can be present and/or expressed at different levels in the biological sample.
The system comprises a flow cell body, first reservoir, and a second reservoir. The flow cell body comprises a bottom layer and a top layer defining a fluidic channel therebetween. The fluidic channel extends along the flow cell body and has an inlet at a first side of the flow cell body and an outlet at a second side of the flow cell body, and a central portion disposed therebetween. The first reservoir is disposed proximate to and in fluidic communication with the inlet. The first reservoir includes at least one sidewall formed in a portion of the top layer of the flow cell body that defines an opening configured to receive at least one reagent. The second reservoir is formed in the top layer and comprises a base that is optically clear. The bottom layer is configured to receive a substrate having a biological sample disposed thereon.
The present disclosure provides methods, systems, compositions, and kits for analyzing target molecules, including using probes comprising a plurality of components for analyzing target molecules in situ in a sample.
The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures such as rolling circle amplification products in the biological sample.
The system comprises a substrate configured to receive a sample, a removable lid, a gasket, and a well wall. The removable lid has a fluidic inlet configured to receive at least one fluidic reagent proximate a first side of the removable lid, and a fluidic outlet proximate a second side of the removable lid. The gasket is disposed on the bottom surface of the removable lid or on the substrate. The well wall is disposed on the substrate and extends around the substrate such that the well and the substrate define an open well. The removable lid and the substrate are configured to translate relative to one another between a coupled configuration and an uncoupled configuration.
The present disclosure relates generally to engineered nucleic acid processing enzymes, based on DNA polymerases (e.g., engineered family B polymerases), and derivatives thereof having reverse transcriptase activity and substantially lacking strand displacement activity; kits comprising the engineered family B polymerases; and methods of generating and using the engineered family B polymerases.
Provided herein are methods, compositions, and kits for the spatial analysis of target nucleic acids in biological samples by their 5′ end. An exemplary method includes: contacting a biological sample with a primer that hybridizes the target nucleic acid; hybridizing the primer to the target nucleic acid and extending using the target nucleic acid as a template to generate an extension product; incorporating a non-templated polynucleotide sequence including at least three nucleotides to the 3′ end of the extension product; hybridizing the polynucleotide sequence of the extension product to a capture domain on an array including a plurality of capture probes that include a spatial barcode and the capture domain; and determining the spatial barcode sequence, or complement thereof, and all or a portion of the extension product, or complement thereof, and using the determined sequences to determine the location of the target nucleic acid in the biological sample. The non-templated polynucleotide sequence may be C-C-C or C-G-C introduced by terminal transferase or may be introduced by SMART technology using reverse transcriptase.
C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
There is provided an assembly for mounting a plurality of optical filters, the assembly comprising: a frame comprising a first portion for securing a first optical filter and a second portion for securing a second optical filter; a first shaft connected to the frame, wherein the first shaft is configured to receive a torque from a motor and rotate the frame about a rotation axis of the first shaft; an alignment member coupled to the first shaft, wherein the alignment member comprises at least one alignment surface configured to align with at least one reference surface of an optical bench; and a clamping member configured to clamp the alignment member against the at least one reference surface. There is also provided a system comprising the assembly, a method for mounting the assembly onto an optical bench, and a method of using the assembly
The present disclosure in some aspects relates to methods for assessing multi-modal in situ transcriptomics by combining microscopy and sequencing technologies and methods. In some aspects, the methods provided herein involve analyzing one or more analyte panels in a sample using a first imaging modality or set of imaging modalities. Based on said analysis, a different analyte panel and/or one or more different imaging modalities can be selected for subsequent analysis.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
48.
METHODS AND COMPOSITIONS FOR IN SITU ANALYSIS OF V(D)J SEQUENCES
The present disclosure relates in some aspects to methods for analyzing antigen receptor transcripts in a biological sample. In some aspects, nucleic acid molecules are generated from V(D)J transcripts in situ in the biological sample to enrich molecules comprising V(D)J joins. In some aspects, the presence, amount, and/or identity of a plurality of V(D)J transcripts are analyzed in situ. Also provided are oligonucleotides, sets of oligonucleotides, compositions, and kits for use in accordance with the methods.
The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.
The present disclosure relates in some aspects to methods and compositions for in situ analysis involving catalytic de-crosslinking of biological samples.
The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures such as rolling circle amplification products in the biological sample.
Methods for determining a location of a feature in a spatial array with features include: (a) providing an array with a first set of one or more features immobilized on a substrate, a first feature of the first set having a first barcoded oligonucleotide with a first spatial barcode and a first constant sequence, and a second set of one or more features immobilized on the substrate, a second feature of the second set having a second barcoded oligonucleotide with a second spatial barcode and a second constant sequence; (b) attaching the first constant sequence to the second constant sequence to generate a nucleic acid product; (c) determining all or a portion of a sequence of the nucleic acid product or a complement thereof; and (d) associating the second barcoded oligonucleotide with the first barcoded oligonucleotide in the nucleic acid product.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
(1) Reagents, assays, enzymes, labeled and unlabeled nucleic acids; antibodies for in vitro screening and labeling of nucleic acids and proteins within tissue samples; buffer solutions for scientific and medical research purposes; kits comprised of reagents for biological analysis for medical research and scientific research purposes; kits comprised of reagents and single-use laboratory bottles and laboratory pipette tips for scientific and medical research purposes; chemical, biochemical and biological preparations for scientific and medical research purposes; combinations of multiple biochemical reagents commonly known as probes, each targeted to one or more biological analytes for detection of those biological analytes for scientific and medical research purposes.
(2) Laboratory equipment, namely, instruments for detection of biological molecules in tissue samples, visualization of cells, and data analysis for scientific and medical research purposes, namely, in situ analyzers; recorded and downloadable computer software for the operation and control of scientific and medical research instruments; recorded and downloadable computer software for processing, qualifying, quantifying, imaging, analysis or storage of medical and scientific research data and results regarding the spatial location or quantities of biological molecules in tissue samples; kits comprised of reagents for scientific and medical research purposes.
Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate.
The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address issues associated with maintaining localization of analytes or products thereof at locations of a sample. In some aspects, a method disclosed herein for amplification provides improved localization of corresponding signals for detecting analytes in a sample.
In some aspects, the present disclosure relates to methods for reducing the detection of false positive ligation events. In some aspects, the method comprises use of a double split (or “split split”) probe. The methods herein have particular applicability in reducing the detection of false positive ligation events when using ligases that have high ligation efficiency but low specificity (e.g., SplintR® ligase). Also provided are kits comprising probes for use in such methods.
Provided herein are kits, systems and methods for analyzing analytes from a biological sample. The system includes an upper housing configured to receive a sample substrate and a thermal element configured to control a temperature of the sample substrate. The system includes a lower housing and an alignment mechanism coupling the upper housing to the lower housing. The alignment mechanism is configured to move the upper housing, the lower housing, or both into an arrangement having an open configuration, a closed configuration, or an intermediate configuration therebetween. The thermal element is configured to cool the sample substrate.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/25 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving enzymes not classifiable in groups
C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
C12Q 1/6816 - Hybridisation assays characterised by the detection means
Provided herein are methods of identifying methylation status of a nucleic acid, e.g., RNA in a biological sample. Also provided herein are methods for identifying the methylation status of RNA in a biological sample with spatial technology to identify the location of a methylated RNA in the biological sample.
The present disclosure generally relates to methods and compositions for in situ analysis or detection of analytes in a biological sample. More specifically, the present disclosure relates to methods for reducing autofluorescence in tissue samples, methods for analyzing tissue samples, and compounds for use in the same. The methods and compounds of the present disclosure may be especially suitable for analytical methods employing fluorescence in situ hybridization techniques over multiple cycles of imaging.
Provided herein are methods, kits and compositions for detecting an analyte of interest to interrogate spatial gene expression in a sample using templated ligation.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase
Provided herein are methods of interrogating spatial gene expression in a sample using substrates having sequencing pores. The disclosed methods allow for spatial analysis of analytes from biological samples using a pore-based sequencing approach and without the need for a barcoded spatial array. In some embodiments, an analyte or intermediate agent thereof, is released from a biological sample and directly sequenced by traversing through pores of a sequencing array including a plurality of pores, e.g., nanopores. In some embodiments, light or other stimuli is used to release an analyte or intermediate agent thereof from a specific region of interest in the biological sample followed by sequencing using sequencing array including a plurality of pores.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Reagents, assays, enzymes, labeled and unlabeled nucleic acids; antibodies for in vitro screening and labeling of nucleic acids and proteins within tissue samples; buffer solutions for scientific and medical research purposes; kits comprised of reagents for biological analysis for medical research and scientific research purposes; kits comprised of reagents and single-use laboratory bottles and laboratory pipette tips for scientific and medical research purposes; chemical, biochemical and biological preparations for scientific and medical research purposes; combinations of multiple biochemical reagents commonly known as probes, each targeted to one or more biological analytes for detection of those biological analytes for scientific and medical research purposes Laboratory equipment, namely, instruments for detection of biological molecules in tissue samples, visualization of cells, and data analysis for scientific and medical research purposes, namely, in situ analyzers; recorded and downloadable computer software for the operation and control of scientific and medical research instruments; recorded and downloadable computer software for processing, qualifying, quantifying, imaging, analysis or storage of medical and scientific research data and results regarding the spatial location or quantities of biological molecules in tissue samples; kits comprised of reagents for scientific and medical research purposes
67.
METHOD FOR TRANSPOSASE-MEDIATED SPATIAL TAGGING AND ANALYZING GENOMIC DNA IN A BIOLOGICAL SAMPLE
The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising performing extension of a target ribonucleic acid (RNA). In some aspects, RNA cutting enzyme and/or a nucleic acid oligonucleotide are used to generate a free 3′ end of the target RNA for an extension reaction.
An illumination device includes a first illumination source arranged to output first illumination light, a second illumination source arranged to output second illumination light, a first collector optic arranged to collect the first illumination light, a second collector optic arranged to collect the second illumination light, a field stop arranged to provide an aperture for light from the first collector optic and second collector optic, and a field optic arranged to image the field stop. The first collector optic is arranged to substantially collimate the first illumination light, and the second collector optic is arranged to form an image of the second illumination source between the second collector optic and the field optic, before or after the field stop so that the image of the second illumination source is defocussed at the field stop.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/25 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving enzymes not classifiable in groups
C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
C12Q 1/6816 - Hybridisation assays characterised by the detection means
Methods, systems, and kits for sequencing a template nucleic acid molecule using a catalyst-scaffold complex are provided. In some aspects, the catalyst-scaffold complex comprises a palladium catalyst that deblocks allyl groups on reversibly terminated nucleotides for use in a sequencing reaction, such as an in situ sequencing reaction in a sample comprising cells and/or cell nuclei. In some aspects, nucleic acid molecules such as rolling circle amplification products in a cell or tissue sample are sequenced in situ using a catalyst-scaffold complex disclosed herein for deprotecting reversibly terminated nucleotides.
A microfluidic system for manipulating particles in a fluid is provided. The system includes a microfluidic chip having at least one channel and at least one filter feature, wherein the filter feature includes a field of physical obstacles configured and arranged to remove physical contaminants associated with the particles. The filter features are particularly suited to remove contaminants associated with gel beads manipulated by microfluidic handling.
Provided herein are systems and methods for analyzing nucleic acids. The present disclosure relates in aspects to methods of detecting an RNA molecule suspected of having a modified nucleotide. The method can further comprise detecting a location of the modified nucleotide on the RNA molecule.
Methods, systems, and kits for sequencing a template nucleic acid molecule using a modified nucleotide molecule including a peptide spacer are provided. In some aspects, the modified nucleotide molecules are used in a sequencing reaction, such as an in situ sequencing reaction.
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
75.
SYSTEMS AND METHODS FOR DELIVERING REAGENTS TO A FLOW CELL
A system for delivering a plurality of reagents into a closed flow cell includes one or more reservoirs comprising reagents, a pump configured to cause a flow of the plurality of reagents, an aspiration device coupled to a first fluid channel, a closed flow cell having an inlet and an outlet, where the inlet is coupled to an end of the first fluid channel, and a de-bubbler coupled to the first fluid channel upstream of the closed flow cell. The de-bubbler is configured to divert one or more bubbles from the first fluid channel.
The present disclosure relates in some aspects to methods, systems, and kits for using diphosphonic acid to promote N—O bond cleavage in a 3′ O—NH2 nucleotide in a cell or tissue sample. In some aspects, diphosphonic acid is used to promote N—O bond cleavage in a 3′ O—NH2 blocked reversible terminator during multiple cycles of a nucleic acid sequencing reaction in a cell or tissue sample. In some embodiments, the chemical reaction of the 3′ O—NH2 blocked reversible terminator with diphosphonic acid releases free alcohols and phosphoric acid derivatives, which are not damaging to the cell or tissue sample.
Methods for strand-displacement amplification of a target nucleic acid have been developed. Compositions for use according to the methods are also provided. The methods typically include steps of removing, hybridizing and extending a selectively removable or digestible primer with a strand-displacing DNA polymerase once or more than once to provide a multiplicity of copies of the target nucleic acid. Methods for strand-displacement amplification of single or double-stranded target DNA molecules are provided. In some forms, when the methods include amplification of a double-stranded nucleic acid, the methods employ one or more adapter handles that perform the function of providing a removable region on a single strand of the ds target. Compositions and kits of oligonucleotide primers and double-stranded nucleic acid adapters including selectively removable regions are also provided for use in the described methods.
Compositions and methods for analysis of protein expression at the single cell level are described. The single cell proteomic technology described herein implements peptide barcode molecules to uniquely label all of the proteins and/or polypeptides present in a single cell, whereby all of the proteins/polypeptides (proteome) present in a single intact cell are uniquely labeled with a peptide barcode molecule in a partition. Polypeptides from a single cell can be uniquely barcoded and via protein sequencing, such as nanopore sequencing. Proteomic analysis of the protein sequencing data elucidates the entire proteome that was expressed in the single cell.
Provided herein are methods and compositions for mRNA fragment-based gene expression profiling in fixed samples. In some aspects, provided herein are methods that leverage fixation-induced mRNA fragmentation and fragmented mRNA-specific ligation biochemistry in single-cell sequencing assays applied to fixed cells. Also provided are related compositions, kits, and systems.
The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. The nucleic acid molecule may be a nucleic acid molecule associated with CRISPR, (e.g., a guide RNA). A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule such as a guide RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.
Systems and methods of identifying antigen-specific cells include obtaining a representation, for each respective immunogenic feature in a plurality of features, of a corresponding count of the respective feature bound to each immune cell in a population of cells. The immune cells are clustered using the representation to identify a plurality of clusters, each including a different subset of the plurality of cells. The total number of unique clonotypes and the total number of clonotypes detected within the subset of cells represented by a particular cluster is determined. This total number of unique clonotypes and total number of clonotypes are used, together with a distribution of a corresponding count of a first immunogenic feature bound to each cell within the subset of cells represented by a particular cluster, to determine whether the subset of cells represented by the respective cluster is antigen-specific for the first immunogenic feature.
G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
Methods, systems, and kits for sequencing a template nucleic acid molecule using O-modified nucleotide molecules including a deoxyribose oligomer spacer are provided. In some aspects, the O-modified nucleotide molecules are used in a sequencing reaction, such as an in situ sequencing reaction.
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.
The present disclosure relates generally to compositions, methods, and systems for the characterization of antigen-binding molecules (e.g., antibodies) in biological samples. This characterization permits the identification of the ABM that bind to regions of interest, or the mapping of ABMs according to their binding to specific regions of interest, of an antigen. Understanding the binding characteristics of ABMs at a region of interest level may facilitate the identification and production of immunotherapeutic molecules having desired properties.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
86.
METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING
The present disclosure relates in some aspects to methods, systems, and kits for sequencing a template nucleic acid molecule using one or more polymerase-luciferase fusion proteins. In some embodiments, different types of polymerase-luciferase fusion proteins and are sequentially contacted with a template nucleic acid in the presence of different types of nucleotides under conditions that stabilize a ternary complex between a given polymerase-luciferase fusion protein, the template nucleic acid molecule, and a nucleotide when the nucleotide is complementary to the template nucleic acid. By imaging the sample to detect luminescence, the base of the template nucleic acid can be identified.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C07K 14/435 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase
A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
The present disclosure relates in some aspects to methods and compositions for generating a library of nucleic acids for analysis. In some aspects, a plurality of RNAs are processed and analyzed in situ in a sample or used to generate a plurality of barcoded nucleic acid molecules for analysis. Also provided are oligonucleotides, a plurality of free nucleotides, detection reagents, compositions, and systems for use in accordance with the methods.
The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.
Methods and compositions for performing a rolling circle amplification (RCA) reaction using circularized template comprising identifier sequences are provided. Sequencing is performed on the RCA product using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate an extension product.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
Provided herein are methods of determining a location or presence of a target analyte in a biological sample by detecting oligonucleotide-conjugated binding agents.
The present disclosure relates in some aspects to methods, compositions, and kits of processing or analyzing a sample. A method for processing a sample may comprise providing probes with barcodes to generate a composite barcode, detecting the barcodes to determine a spatial location and hybridizing probes to analytes (e.g., an RNA molecule) and performing sequencing.
in situin situ in a sample. Also provided are oligonucleotides for hybridization, sets of oligonucleotides, sequencing reagents, compositions, and systems for use in accordance with the methods.
Provided herein are methods, systems, and kits for detecting analytes of interest from biological samples using tagmentation. The methods include tagmenting DNA/RNA hybrids that include an mRNA molecule and a barcode nucleic acid molecule to generate a plurality of tagmented fragments, and separating a first tagmented fragment including an end portion of the mRNA and a barcode from other tagmented fragments.
Provided herein are methods, compositions, and kits for detecting analytes of interest from biological samples using tagmentation. The method comprises: (a) hybridising a nucleic acid analyte to a capture probe on an array, wherein the capture probe comprises: (i) a spatial barcode and (ii) a capture domain; (b) extending the capture probe using the nucleic acid analyte as a template, thereby generating a barcoded nucleic acid molecule on the array, wherein the barcoded nucleic acid molecule comprises a complement of the sequence of the nucleic acid analyte; and (c) tagmenting the barcoded nucleic acid molecule or a derivative thereof using a transposome comprising a transposase to insert a transposon end sequence into the barcoded nucleic acid molecule or the derivative thereof, thereby generating a barcoded nucleic acid fragment, wherein the barcoded nucleic acid fragment comprises: (i) the barcode, (ii) the transposon end sequence, and (iii) at least a portion of a sequence of the nucleic acid analyte or a complement thereof.
Provided herein are methods for capturing an analyte from a first region of interest of a biological sample on a substrate, where the biological sample comprises the first region of interest and a second region, and where the method includes contacting the second region with a sealant in order to create a hydrophobic seal thereby preventing an interaction between an analyte from the second region with a capture domain of a capture probe.
The disclosure provides systems and methods for droplet processing. For example, a method can include providing a first droplet and a second droplet. In some cases, the first droplet may have a first concentration of a reagent and the second droplet may have a second concentration of the reagent. The second droplet may comprise a bead or a biological particle. The method can also include subjecting the first droplet and the second droplet to conditions sufficient to transfer the reagent from the first droplet to the second droplet, thereby decreasing the first concentration in the first droplet and increasing the second concentration in the second droplet.
An electrophoretic system is provided for analyte capture from a biological sample. The electrophoretic system can be used to permeabilize the sample to allow analytes to be released from the sample. For example, the sample can be contacted with capture probes attached to a substrate, and an electric field created by the electrophoretic system can cause analytes to be released from the cell, and effectively migrate toward and bind to the capture probes attached to the substrate.
