Patents Assigned to Takara Bio USA, Inc.
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Patent number: 11959078Abstract: Methods of preparing a next generation sequencing (NGS) library from a ribonucleic acid (RNA) sample are provided. Aspects of the methods include combining the RNA sample with a first strand cDNA primer and a template switch oligonucleotide under first strand cDNA synthesis conditions, where one of the first strand cDNA primer and the template switch oligonucleotide includes a first post-tagmentation amplification primer binding domain. The resultant product is subjected to amplification conditions sufficient to produce a double stranded cDNA, which is then tagmented with a transposome that includes a second post-tagmentation amplification primer binding domain. The tagmented sample is then subjected to amplification conditions using first and second post-tagmentation amplification primers that include sequencing platform adapter constructs to produce a NGS library. Aspects of the invention further include compositions produced by the methods and kits that find use in practicing the methods.Type: GrantFiled: October 21, 2020Date of Patent: April 16, 2024Assignee: Takara Bio USA, Inc.Inventors: Cynthia Chang, Magnolia Bostick
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Patent number: 11884963Abstract: Provided are methods of depleting a target nucleic acid from an initial collection of nucleic acids. Aspects of the methods include contacting the initial collection with a nucleic acid guided nuclease specific for the target nucleic acid in a manner sufficient to deplete the target nucleic acid from the initial collection. Depending on a given application, depletion of a target nucleic acid may vary, e.g., where depleting may include cleaving a target nucleic acid in, or selectively separating a target nucleic acid from, the initial collection of nucleic acids. Also provided are compositions and kits for practicing embodiments of the methods.Type: GrantFiled: April 20, 2021Date of Patent: January 30, 2024Assignee: Takara Bio USA, Inc.Inventors: Andrew Alan Farmer, Craig Betts, Nathalie Bolduc
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Patent number: 11667952Abstract: Provided are methods of producing product nucleic acids involving the use of oligonucleotides that are modified by the application of a stimulus. Aspects of such methods may include producing product nucleic acids using de-activatable oligonucleotides that are deactivated by a de-activating stimulus, as well as methods that may include producing product nucleic acids using activatable oligonucleotides that are activated by an activating stimulus and de-activatable oligonucleotides that are deactivated by a de-activating stimulus. Also provided are kits, compositions and devices that include de-activatable oligonucleotides or activatable and de-activatable oligonucleotides, e.g., for use in performing the methods as described herein.Type: GrantFiled: August 23, 2018Date of Patent: June 6, 2023Assignee: Takara Bio USA, Inc.Inventor: Kazuo Tori
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Patent number: 11661628Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: August 10, 2017Date of Patent: May 30, 2023Assignee: Takara Bio USA, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Patent number: 11643635Abstract: Protein enriched micro-vesicles and methods of making and using the same are provided. Aspects of the methods include maintaining a cell having a membrane-associated protein comprising a first dimerization domain and a target protein having a second dimerization domain under conditions sufficient to produce a micro-vesicle from the cell, wherein the micro-vesicle includes the target protein. Also provided are cells, reagents and kits that find use in making the micro-vesicles, as well as methods of using the micro-vesicles, e.g., in research and therapeutic applications.Type: GrantFiled: August 21, 2020Date of Patent: May 9, 2023Assignee: Takara Bio USA, Inc.Inventors: Michael Haugwitz, Thomas Patrick Quinn, Andrew Alan Farmer, Montserrat Morell Fernández
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Patent number: 11643681Abstract: Apparatus, systems, chips, and methods of performing a large number of simultaneous chemical reactions are provided herein. The chips of the invention comprise addressable units that can be addressed according to the temperature of the reaction to be run. The subject apparatus, systems, and chips are particularly suited for performing polymerase chain reactions on thousands of nucleic acid sequences, up to and including sequences of an entire genuine of an organism of interest.Type: GrantFiled: March 9, 2018Date of Patent: May 9, 2023Assignee: Takara Bio USA, Inc.Inventors: Victor Joseph, Amjad Huda, Alnoor Shivji
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Patent number: 11492663Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: February 15, 2019Date of Patent: November 8, 2022Assignee: Takara Bio USA, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Patent number: 11479806Abstract: Methods of producing an amplified double stranded deoxyribonucleic acid (dsDNA) from a nucleic acid sample are provided. Aspects of the methods include amplifying using a single product nucleic acid primer and a template switch oligonucleotide to produce an amplified dsDNA product. Compositions and kits for use in performing the methods are also provided.Type: GrantFiled: November 8, 2017Date of Patent: October 25, 2022Assignee: Takara Bio USA, Inc.Inventors: Kazuo Tori, Magnolia Bostick, Andrew Farmer
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Patent number: 11460405Abstract: Provided are methods, devices, assemblies, and systems for dispensing into the wells of a multi-well device and imaging such wells from multiple Z-planes. Multi-Z imaging of the present methods and systems may allow for the detection of wells of a multi-well device that contain a desired number of cells. Also provided are methods, devices, assemblies, and systems for processing cell-containing wells of a multi-well device identified through the use of multi-Z imaging.Type: GrantFiled: July 20, 2017Date of Patent: October 4, 2022Assignee: Takara Bio USA, Inc.Inventors: Patricio A. Espinoza Vallejos, Syed A. Husain, Chun-Wah Lin, Hermann Hubschle
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Patent number: 11371087Abstract: The present disclosure provides methods, compositions, and systems employing blocked primers. Aspects of the disclosure include providing a blocked primer reaction mixture that includes a blocked primer and a template nucleic acid component from a single cell; unblocking the blocked primer to produce an active primer reaction mixture and subjecting the activated primer reaction mixture to primer extension conditions, such as nucleic acid amplification conditions.Type: GrantFiled: June 8, 2017Date of Patent: June 28, 2022Assignee: Takara Bio USA, Inc.Inventors: Thomas D. Schaal, Jude Menlo Dunne, Maithreyan Srinivasan, Alain Mir
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Patent number: 11149303Abstract: Provided are methods of depleting a target nucleic acid in a sample. The methods include contacting a target nucleic acid with two or more polymers that specifically hybridize to the target nucleic acid, and cleaving the hybridized regions of the target nucleic acid to deplete the target nucleic acid in the sample. Kits for practicing the subject methods are also provided.Type: GrantFiled: August 9, 2019Date of Patent: October 19, 2021Assignee: Takara Bio USA, Inc.Inventors: Andrew Alan Farmer, Ian B. Oglesby, Magnolia Bostick, Steve Oh
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Patent number: 11125752Abstract: The present disclosure provides methods, device, assemblies, and systems for dispensing and visualizing single cells. For example, provided herein are systems and methods for dispensing a dispense volume into a plurality of wells of a multi-well device, where, on average, a pre-determined number of cells (e.g., 1-20) are present in the dispense volume, and determining, via a cellular label, the number of cells present in each of the plurality of wells. Such dispensing and cell detection may be repeated a number of times with respect to wells identified as having less than the pre-determined number of cells in order increase the number wells in the multi-well device containing the desired number (e.g., a single cell).Type: GrantFiled: March 30, 2020Date of Patent: September 21, 2021Assignee: Takara Bio USA, Inc.Inventors: Alain-Albert Mir, Thomas D. Schaal, Chun-Wah Lin, Shanavaz Loharasp D. Nasarabadi, Jude Dunne, Maithreyan Srinivasan, Patricio A. Espinoza-Vallejos
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Patent number: 11124828Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template nucleic acid, a template switch oligonucleotide, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template nucleic acid and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid including a region polymerized from the dNTPs by the polymerase. The methods further include attaching sequencing platform adapter constructs to ends of the product nucleic acid or a derivative thereof. Aspects of the invention further include compositions and kits.Type: GrantFiled: August 2, 2019Date of Patent: September 21, 2021Assignee: Takara Bio USA, Inc.Inventors: Craig Betts, Andrew Alan Farmer
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Patent number: 11103831Abstract: Spin columns that include a poly(acid) membrane separation matrix are provided. Also provided are kits that include the subject devices, as well as methods of using the devices, e.g., in sample preparation (such as protein purification) protocols.Type: GrantFiled: December 12, 2018Date of Patent: August 31, 2021Assignee: Takara Bio USA, Inc.Inventors: George G. Jokhadze, Sayantan Mitra
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Patent number: 11072823Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: GrantFiled: December 21, 2018Date of Patent: July 27, 2021Assignee: Takara Bio USA, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
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Patent number: 11001882Abstract: Provided are methods of producing a product nucleic acid. The methods include combining a template deoxyribonucleic acid (DNA), a polymerase, a template switch oligonucleotide, and dNTPs into a reaction mixture. The components are combined into the reaction mixture under conditions sufficient to produce a product nucleic acid that includes the template DNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.Type: GrantFiled: June 27, 2016Date of Patent: May 11, 2021Assignee: Takara Bio USA, Inc.Inventors: Craig Betts, Andrew Alan Farmer, Nathalie Bolduc
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Patent number: 10988796Abstract: Provided are methods of depleting a target nucleic acid from an initial collection of nucleic acids. Aspects of the methods include contacting the initial collection with a nucleic acid guided nuclease specific for the target nucleic acid in a manner sufficient to deplete the target nucleic acid from the initial collection. Depending on a given application, depletion of a target nucleic acid may vary, e.g., where depleting may include cleaving a target nucleic acid in, or selectively separating a target nucleic acid from, the initial collection of nucleic acids. Also provided are compositions and kits for practicing embodiments of the methods.Type: GrantFiled: October 8, 2018Date of Patent: April 27, 2021Assignee: Takara Bio USA, Inc.Inventors: Andrew Alan Farmer, Craig Betts, Nathalie Bolduc
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Patent number: 10961529Abstract: Methods of barcoding nucleic acids, such as genomic DNA, are provided herein. In some embodiments, a fragment of genomic DNA may comprise a first and a second barcode.Type: GrantFiled: November 7, 2018Date of Patent: March 30, 2021Assignee: Takara Bio USA, Inc.Inventors: Takao Kurihara, Emmanuel Kamberov, Tim Tesmer, John Langmore
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Patent number: 10954510Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3? hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.Type: GrantFiled: March 24, 2017Date of Patent: March 23, 2021Assignee: Takara Bio USA, Inc.Inventors: Craig Betts, Steve Oh, George G. Jokhadze, Nathalie Bolduc
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Patent number: 10941397Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3? hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.Type: GrantFiled: September 5, 2014Date of Patent: March 9, 2021Assignee: Takara Bio USA, Inc.Inventors: Craig Betts, Steve Oh, George Jokhadze, Nathalie Bolduc