A microwell array specifically designed for culturing organoids is provided along with a system to enable automated imaging, identification, and isolation of individual organoids. The microwells of the microarray include a releasable cellraft that enables the automated release and transfer of selected organoids present on the cellrafts to a separate collection plate. Organoids grown on the microarray can be reliably tracked, imaged, and phenotypically analyzed by the instrument system in brightfield and fluorescence as they grow over time, then released and transferred fully intact for use in downstream applications. The use of the system is demonstrated using mouse hepatic and pancreatic organoids for single-organoid imaging, clonal organoid generation, parent organoid subcloning, and single-organoid RNA extraction for downstream gene expression or transcriptomic analysis.
A microwell array specifically designed for culturing organoids is provided along with a system to enable automated imaging, identification, and isolation of individual organoids. The microwells of the microarray include a releasable cellraft that enables the automated release and transfer of selected organoids present on the cellrafts to a separate collection plate. Organoids grown on the microarray can be reliably tracked, imaged, and phenotypically analyzed by the instrument system in brightfield and fluorescence as they grow over time, then released and transferred fully intact for use in downstream applications. The use of the system is demonstrated using mouse hepatic and pancreatic organoids for single-organoid imaging, clonal organoid generation, parent organoid subcloning, and single-organoid RNA extraction for downstream gene expression or transcriptomic analysis.
The Trustees of Columbia University in the City of New York (USA)
Inventor
Duvall, Jacquelyn
Thompson, Brandon
Sims, Peter Alan
Yuan, Jinzhou
Liu, Zhouzerui
Mizrak, Dogukan
Gebhart, Steven C.
Boone, Peter Glyn
Abstract
Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.
A microwell array specifically designed for culturing organoids is provided along with a system to enable automated imaging, identification, and isolation of individual organoids. The microwells of the microarray include a releasable cellraft that enables the automated release and transfer of selected organoids present on the cellrafts to a separate collection plate. Organoids grown on the microarray can be reliably tracked, imaged, and phenotypically analyzed by the instrument system in brightfield and fluorescence as they grow over time, then released and transferred fully intact for use in downstream applications. The use of the system is demonstrated using mouse hepatic and pancreatic organoids for single-organoid imaging, clonal organoid generation, parent organoid subcloning, and single-organoid RNA extraction for downstream gene expression or transcriptomic analysis.
THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK (USA)
Inventor
Duvall, Jacquelyn
Thompson, Brandon
Sims, Peter, Alan
Yuan, Jinzhou
Liu, Zhouzerui
Mizrak, Dogukan
Gebhart, Steven, C.
Boone, Peter, Glyn
Abstract
Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.
The University of North Carolina at Chapel Hill (USA)
Inventor
Gebhart, Steven C.
Mcclellan, Robert W.
Trotta, Nicholas C.
Allbritton, Nancy L.
Attayek, Peter Joseph
Armistead, Paul Michael
Abstract
Embodiments of the disclosed subject matter provide an automated method and system to isolate and collect cells using computerized analysis of images of cells and their surroundings obtained from a digital imaging device or system. Embodiments of the disclosed subject matter make use of a “microwell array,” which can comprise a formed, elastomeric grid of indentations or “wells.” Many, most, or all of the wells in a microwell array can contain a releasable, microfabricated element, which can be referred to as a “raft.” Embodiments of the disclosed subject matter provide a system and method for cell collection that includes computerized identification and collection of rafts with isolated single cells or a specific group or groups of cells, eliminating the need for continuous human identification and selection.
09 - Scientific and electric apparatus and instruments
Goods & Services
Scientific apparatuses, instruments and devices, namely automated systems for cell imaging analysis, sorting, and isolation from a microwell array device comprising computers, downloadable computer software for controlling cell imaging and isolation instrumentation, downloadable computer software for cell image analysis, microscopes with brightfield and fluorescence imaging capabilities as well as motorized stages and stage adapters for the microwell array device, needles and magnetic wands being component parts of cell isolation instrumentation, and microwell array devices comprised of single and multi-reservoir plates and dishes with microwell array formats containing releasable paramagnetic cell-culture surfaces in each microwell for sample preparation, culturing, sorting, isolation, separation, modification, manipulation, and analysis of cells; component parts for scientific apparatuses, instruments and devices, namely microscopes and parts thereof, motorized microscope stages and stage adapters for microwell array devices, needles and magnetic wands being component parts of cell isolation instrumentation, microwell array devices comprised of single and multi-reservoir plates and dishes with microwell array formats containing releasable paramagnetic cell-culture surfaces in each microwell, downloadable computer software for controlling cell imaging and isolation instrumentation, and downloadable computer software for cell image analysis; laboratory apparatus and instruments, in particular computers, downloadable computer software for controlling cell imaging and isolation instrumentation, downloadable computer software for cell image analysis, microscopes with brightfield and fluorescence imaging capabilities as well as motorized stages and stage adapters for microwell array devices, microwell array devices comprised of single and multi-reservoir plates and dishes with microwell array formats containing releasable paramagnetic cell-culture surfaces in each microwell, for use in scientific and medical research
09 - Scientific and electric apparatus and instruments
Goods & Services
Scientific apparatuses, instruments and devices, namely paramagnetic microdevices, in particular, single and multi-reservoir plates and cell culture dishes with microwell array formats for sample preparation, culturing, sorting, isolation, separation, modification, manipulation, and analysis of cells; component parts for scientific apparatuses, instruments and devices, namely paramagnetic microdevices, in particular, single and multi-reservoir plates and cell culture dishes with microwell array formats; laboratory apparatus and instruments, namely paramagnetic microdevices, in particular, single and multi-reservoir plates and cell-culture dishes with microwell array formats for use in scientific and medical research; scientific apparatuses, instruments and devices in the area of cell analysis, namely in particular paramagnetic microdevices, in particular, single and multi-reservoir plates and cell culture dishes with microwell array formats, for collection, separation and isolation of cells for scientific and research purposes
9.
Automated collection of a specified number of cells
The University of North Carolina at Chapel Hill (USA)
Inventor
Gebhart, Steven C.
Mcclellan, Robert W.
Trotta, Nicholas C.
Allbritton, Nancy L.
Attayek, Peter Joseph
Armistead, Paul Michael
Abstract
Embodiments of the disclosed subject matter provide an automated method and system to isolate and collect cells using computerized analysis of images of cells and their surroundings obtained from a digital imaging device or system. Embodiments of the disclosed subject matter make use of a “microwell array,” which can comprise a formed, elastomeric grid of indentations or “wells.” Many, most, or all of the wells in a microwell array can contain a releasable, microfabricated element, which can be referred to as a “raft.” Embodiments of the disclosed subject matter provide a system and method for cell collection that includes computerized identification and collection of rafts with isolated single cells or a specific group or groups of cells, eliminating the need for continuous human identification and selection.
The University of North Carolina at Chapel Hill (USA)
Cell Microsystems, Inc. (USA)
Inventor
Allbritton, Nancy L.
Wang, Yuli
Sims, Christopher E.
Dobes, Nicholas C.
Gebhart, Steven C.
Trotta, Nicholas C.
Abstract
An array of magnetic or paramagnetic micro-elements comprised of polysilsesquioxane is described having ultra-low-autofluorescence and other optical properties to improve microscopic imaging of cells or other objects present on the array. These materials are also amenable to chemical modification allowing surface attachment of affinity capture moieties or chemical reporters for selective binding or analysis of cells, macromolecules or other targets.
The invention discloses diagnostic techniques based on single cell genomics, consisting of obtaining a blood sample, enriching a sub-population of cells present in the blood sample, sequestering individual cells or group of cells from the blood sample, obtaining sequencing data from the sequestered cells or group of cells, using genetic variant information to determine the provenance of the cells, and genetically analyzing the cells of the correct provenance to provide a diagnostic readout. Using the cell-based testing techniques of the invention, the number of false positives is greatly reduced when compared to cell-free DNA (cfDNA) based traditional testing techniques. The invention may be effectively employed for non-invasive prenatal (NIPT) diagnostics, oncological testing and other diagnostic procedures.
THE UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL (USA)
Inventor
Gebhart, Steven, C.
Mcclellan, Robert, W.
Trotta, Nicholas, C.
Allbritton, Nancy, L.
Attayek, Peter, Joseph
Armistead, Paul, Michael
Abstract
Embodiments of the disclosed subject matter provide an automated method and system to isolate and collect cells using computerized analysis of images of cells and their surroundings obtained from a digital imaging device or system. Embodiments of the disclosed subject matter make use of a "microwell array," which can comprise a formed, elastomeric grid of indentations or "wells." Many, most, or all of the wells in a microwell array can contain a releasable, microfabricated element, which can be referred to as a "raft." Embodiments of the disclosed subject matter provide a system and method for cell collection that includes computerized identification and collection of rafts with isolated single cells or a specific group or groups of cells, eliminating the need for continuous human identification and selection.
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
C12M 1/32 - Inoculator or sampler multiple field or continuous type
09 - Scientific and electric apparatus and instruments
Goods & Services
Scientific apparatuses, instruments and devices, namely, automated platforms for cytometric or fluorescent imaging of cells in an array format and attachments for microscopes for use with cells in an array format for sample preparation, culturing, sorting, isolation, separation, modification, manipulation, and analysis of cells; Component parts for scientific apparatuses, instruments and devices, namely, release probes, microscope attachments, optical and imaging parts, mechanical stages, microwell arrays, magnetic wands, cell culture dishes, multi-reservoir plates, and automated platforms, for cytometric or fluorescent imaging of cells in an array format and attachments for microscopes for use with cells in an array format for use in scientific and medical research of cells; laboratory apparatus and instruments, in particular plates, platforms, cell-culture dishes, microwell arrays, magnetic multi-well plates being in array format, vessels, needles, and wands for use in scientific and medical research of cells; Scientific apparatuses, instruments and devices in the area of cell analysis, namely, magnetic microdevices, in particular, single and multi-reservoir plates and cell culture dishes with microwell array formats, for culturing, sorting, collection, separation and isolation of cells for scientific and medical research purposes; Chemical, biochemical, and biotechnological apparatuses, namely, automated platforms for fluorescent imaging of cells in an array format for scientific and medical research purposes for sample preparation, isolation, separation, modification, manipulation, and analysis of cells
09 - Scientific and electric apparatus and instruments
Goods & Services
Scientific apparatuses, instruments and devices, namely, automated platforms for cytometric and fluorescent imaging of cells in an array format and attachments for microscopes for use with cells in an array format for sample preparation, culturing, sorting, isolation, separation, modification, manipulation, and analysis of cells; Component parts for scientific apparatuses, instruments and devices, namely, release probes, microscope attachments, optical and imaging parts, mechanical stages, microwell arrays, magnetic wands, cell culture dishes, multi-reservoir plates, and automated platforms for cytometric imaging of cells in an array format and attachments for microscopes for use with cells in an array format; laboratory apparatus and instruments, in particular plates, platforms, cell-culture dishes, microwell arrays, magnetic multi-well plates being in array format, vessels, needles, and wands for use in scientific and medical research of cells; Scientific apparatuses, instruments and devices in the area of cell analysis, namely, magnetic microdevices, in particular, single and multi-reservoir plates and cell culture dishes with microwell array formats, for culturing, sorting, separation and isolation of cells for scientific and medical research; Chemical, biochemical, and biotechnological apparatuses, namely, automated platforms for fluorescent imaging of cells in an array format for scientific and medical research purposes for sample preparation, isolation, separation, modification, manipulation, and analysis of cells
A mount suitable to be mounted to a microscope objective is described with a first member; a second member engaged with the first member; a first configuration where the second member has a first effective diameter; and a second configuration where the second member has a second effective diameter less than the first effective diameter for securably engaging an outer surface of a microscope objective. Methods of using the mount are also disclosed.
The invention discloses diagnostic techniques based on single cell genomics, consisting of obtaining a blood sample, enriching a sub-population of cells present in the blood sample, sequestering individual cells or group of cells from the blood sample, obtaining sequencing data from the sequestered cells or group of cells, using genetic variant information to determine the provenance of the cells, and genetically analyzing the cells of the correct provenance to provide a diagnostic readout. Using the cell-based testing techniques of the invention, the number of false positives is greatly reduced when compared to cell-free DNA (cfDNA) based traditional testing techniques. The invention may be effectively employed for non-invasive prenatal (NIPT) diagnostics, oncological testing and other diagnostic procedures.
THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK (USA)
CELL MICROSYSTEMS, INC. (USA)
Inventor
Duvall, Jacquelyn
Thompson, Brandon
Sims, Peter Alan
Yuan, Jinzhou
Liu, Zhouzerui
Mizrak, Dogukan
Gebhart, Steven C.
Boone, Peter Glyn
Abstract
Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.
THE UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL (USA)
Inventor
Gebhart, Steven C.
Mcclellan, Robert W.
Trotta, Nicholas C.
Allbritton, Nancy L.
Attayek, Peter Joseph
Armistead, Paul Michael
Abstract
Embodiments of the disclosed subject matter provide an automated method and system to isolate and collect cells using computerized analysis of images of cells and their surroundings obtained from a digital imaging device or system. Embodiments of the disclosed subject matter make use of a "microwell array," which can comprise a formed, elastomeric grid of indentations or "wells." Many, most, or all of the wells in a microwell array can contain a releasable, microfabricated element, which can be referred to as a "raft." Embodiments of the disclosed subject matter provide a system and method for cell collection that includes computerized identification and collection of rafts with isolated single cells or a specific group or groups of cells, eliminating the need for continuous human identification and selection.
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
19.
AUTOMATED SYSTEM FOR IMAGING, IDENTIFICATION, AND ISOLATION OF ORGANOIDS
A microwell array specifically designed for culturing organoids is provided along with a system to enable automated imaging, identification, and isolation of individual organoids. The microwells of the microarray include a releasable cellraft that enables the automated release and transfer of selected organoids present on the cellrafts to a separate collection plate. Organoids grown on the microarray can be reliably tracked, imaged, and phenotypically analyzed by the instrument system in brightfield and fluorescence as they grow over time, then released and transferred fully intact for use in downstream applications. The use of the system is demonstrated using mouse hepatic and pancreatic organoids for single-organoid imaging, clonal organoid generation, parent organoid subcloning, and single-organoid RNA extraction for downstream gene expression or transcriptomic analysis.
