CA2976681A1 - Single-cell nucleic acids for high-throughput studies - Google Patents
Single-cell nucleic acids for high-throughput studies Download PDFInfo
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- CA2976681A1 CA2976681A1 CA2976681A CA2976681A CA2976681A1 CA 2976681 A1 CA2976681 A1 CA 2976681A1 CA 2976681 A CA2976681 A CA 2976681A CA 2976681 A CA2976681 A CA 2976681A CA 2976681 A1 CA2976681 A1 CA 2976681A1
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Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
- C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
- B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
- B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
- B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
- B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
- B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
- B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
- B01L3/502761—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/06—Fluid handling related problems
- B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
- B01L2200/0652—Sorting or classification of particles or molecules
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/06—Auxiliary integrated devices, integrated components
- B01L2300/0609—Holders integrated in container to position an object
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0893—Geometry, shape and general structure having a very large number of wells, microfabricated wells
Landscapes
- Chemical & Material Sciences (AREA)
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- General Health & Medical Sciences (AREA)
- Analytical Chemistry (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Physics & Mathematics (AREA)
- Molecular Biology (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Biotechnology (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Biophysics (AREA)
- Dispersion Chemistry (AREA)
- Hematology (AREA)
- Clinical Laboratory Science (AREA)
- Fluid Mechanics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201562126349P | 2015-02-27 | 2015-02-27 | |
| US62/126,349 | 2015-02-27 | ||
| PCT/US2016/019952 WO2016138490A1 (en) | 2015-02-27 | 2016-02-26 | Single-cell nucleic acids for high-throughput studies |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2976681A1 true CA2976681A1 (en) | 2016-09-01 |
Family
ID=56789110
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2976681A Pending CA2976681A1 (en) | 2015-02-27 | 2016-02-26 | Single-cell nucleic acids for high-throughput studies |
Country Status (7)
| Country | Link |
|---|---|
| US (2) | US10190163B2 (enExample) |
| EP (1) | EP3262214B1 (enExample) |
| JP (1) | JP2018509896A (enExample) |
| CN (1) | CN107250445A (enExample) |
| CA (1) | CA2976681A1 (enExample) |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2023037334A1 (en) | 2021-09-13 | 2023-03-16 | Ecole Polytechnique Federale De Lausanne (Epfl) | System and method for single cell phenotypical profiling and deterministic nanoliter-droplet encapsulation and deterministic droplet consortia assemblies |
Families Citing this family (43)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP2414547B1 (en) | 2009-04-02 | 2014-03-12 | Fluidigm Corporation | Multi-primer amplification method for barcoding of target nucleic acids |
| US8835358B2 (en) | 2009-12-15 | 2014-09-16 | Cellular Research, Inc. | Digital counting of individual molecules by stochastic attachment of diverse labels |
| SG194745A1 (en) | 2011-05-20 | 2013-12-30 | Fluidigm Corp | Nucleic acid encoding reactions |
| US10466160B2 (en) | 2011-08-01 | 2019-11-05 | Celsee Diagnostics, Inc. | System and method for retrieving and analyzing particles |
| US9404864B2 (en) | 2013-03-13 | 2016-08-02 | Denovo Sciences, Inc. | System for imaging captured cells |
| EP2739587B1 (en) | 2011-08-01 | 2020-05-27 | Denovo Sciences | Cell capture system |
| US9752181B2 (en) | 2013-01-26 | 2017-09-05 | Denovo Sciences, Inc. | System and method for capturing and analyzing cells |
| US9707562B2 (en) | 2013-03-13 | 2017-07-18 | Denovo Sciences, Inc. | System for capturing and analyzing cells |
| US9856535B2 (en) | 2013-05-31 | 2018-01-02 | Denovo Sciences, Inc. | System for isolating cells |
| US10391490B2 (en) | 2013-05-31 | 2019-08-27 | Celsee Diagnostics, Inc. | System and method for isolating and analyzing cells |
| WO2016138490A1 (en) | 2015-02-27 | 2016-09-01 | Fluidigm Corporation | Single-cell nucleic acids for high-throughput studies |
| KR20180097536A (ko) | 2015-11-04 | 2018-08-31 | 아트레카, 인크. | 단일 세포와 연관된 핵산의 분석을 위한 핵산 바코드의 조합 세트 |
| EP3390658B1 (en) | 2015-12-16 | 2022-08-03 | Standard BioTools Inc. | High-level multiplex amplification |
| US10202641B2 (en) | 2016-05-31 | 2019-02-12 | Cellular Research, Inc. | Error correction in amplification of samples |
| ES2870639T3 (es) | 2016-10-24 | 2021-10-27 | Geneinfosec Inc | Ocultación de información presente en los ácidos nucleicos |
| WO2018148700A1 (en) * | 2017-02-13 | 2018-08-16 | Yale University | High-throughput single-cell polyomics |
| EP4345172A3 (en) | 2017-06-05 | 2024-07-03 | Becton, Dickinson and Company | Sample indexing for single cells |
| SG11201912798VA (en) * | 2017-06-20 | 2020-01-30 | Ubiome Inc | Method and system for library preparation with unique molecular identifiers |
| WO2019046307A1 (en) | 2017-08-29 | 2019-03-07 | Celsee Diagnostics, Inc. | SYSTEM AND METHOD FOR ISOLATING AND ANALYZING CELLS |
| CN111094587B (zh) * | 2017-08-30 | 2024-08-06 | 卡帕生物系统公司 | 转座酶组合物、制备方法和筛选方法 |
| CN112236518A (zh) * | 2018-02-23 | 2021-01-15 | 耶鲁大学 | 单细胞冻融裂解 |
| AU2019262048B2 (en) | 2018-05-03 | 2025-09-04 | Becton, Dickinson And Company | High throughput multiomics sample analysis |
| WO2020036926A1 (en) * | 2018-08-17 | 2020-02-20 | Cellecta, Inc. | Multiplex preparation of barcoded gene specific dna fragments |
| CN118853827A (zh) * | 2018-10-01 | 2024-10-29 | 贝克顿迪金森公司 | 确定5’转录物序列 |
| CN113454234B (zh) | 2019-02-14 | 2025-03-18 | 贝克顿迪金森公司 | 杂合体靶向和全转录物组扩增 |
| US10633693B1 (en) | 2019-04-16 | 2020-04-28 | Celsee Diagnostics, Inc. | System and method for leakage control in a particle capture system |
| US11273439B2 (en) | 2019-05-07 | 2022-03-15 | Bio-Rad Laboratories, Inc. | System and method for target material retrieval from microwells |
| US11578322B2 (en) | 2019-05-07 | 2023-02-14 | Bio-Rad Laboratories, Inc. | System and method for automated single cell processing |
| CN118291246A (zh) | 2019-06-14 | 2024-07-05 | 伯乐实验室有限公司 | 用于自动化单细胞处理和分析的系统和方法 |
| JP2022544101A (ja) * | 2019-08-08 | 2022-10-17 | アンスティチュ ナショナル ドゥ ラ サンテ エ ドゥ ラ ルシェルシュ メディカル | 表現型の規定されたｂ細胞及びｔ細胞のサブセットにおける、ｂ細胞とｔ細胞のトランスクリプトームの分析のためのｒｎａシークエンス法 |
| CN114729392A (zh) * | 2019-09-06 | 2022-07-08 | 10X基因组学有限公司 | 用于对细胞和细胞珠粒进行条形码化的系统和方法 |
| US20230028445A1 (en) * | 2019-10-11 | 2023-01-26 | Black Hawk Genomics, Llc | Identification of genomic structural variants using long-read sequencing |
| GB2589869A (en) * | 2019-12-09 | 2021-06-16 | Univ Oxford Innovation Ltd | Method for whole genome sequencing of picogram quantities of DNA |
| US12445148B2 (en) * | 2020-01-03 | 2025-10-14 | Koninklijke Philips N.V. | System and method for effective compression representation and decompression of diverse tabulated data |
| EP4097228B1 (en) | 2020-01-29 | 2024-08-14 | Becton, Dickinson and Company | Barcoded wells for spatial mapping of single cells through sequencing |
| WO2021173719A1 (en) | 2020-02-25 | 2021-09-02 | Becton, Dickinson And Company | Bi-specific probes to enable the use of single-cell samples as single color compensation control |
| US11504719B2 (en) | 2020-03-12 | 2022-11-22 | Bio-Rad Laboratories, Inc. | System and method for receiving and delivering a fluid for sample processing |
| EP4150118A1 (en) | 2020-05-14 | 2023-03-22 | Becton Dickinson and Company | Primers for immune repertoire profiling |
| EP4407030B1 (en) | 2020-06-02 | 2025-12-17 | Becton, Dickinson and Company | Oligonucleotides and beads for 5 prime gene expression assay |
| US11932901B2 (en) | 2020-07-13 | 2024-03-19 | Becton, Dickinson And Company | Target enrichment using nucleic acid probes for scRNAseq |
| EP4240842B1 (en) * | 2020-11-03 | 2024-12-18 | ACT Genomics (IP) Limited | Targeted sequencing method and kit thereof for detecting gene alteration |
| US12392771B2 (en) | 2020-12-15 | 2025-08-19 | Becton, Dickinson And Company | Single cell secretome analysis |
| US12465910B2 (en) | 2021-12-10 | 2025-11-11 | Bio-Rad Laboratories, Inc. | Compositions, methods, and systems for sample processing with morphology-adjustable functionalized particles |
Family Cites Families (34)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5449602A (en) | 1988-01-13 | 1995-09-12 | Amoco Corporation | Template-directed photoligation |
| US5494810A (en) | 1990-05-03 | 1996-02-27 | Cornell Research Foundation, Inc. | Thermostable ligase-mediated DNA amplifications system for the detection of genetic disease |
| EP2368897B1 (en) | 1996-02-09 | 2016-10-19 | Cornell Research Foundation, Inc. | Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays |
| EP2369007B1 (en) | 1996-05-29 | 2015-07-29 | Cornell Research Foundation, Inc. | Detection of nucleic acid sequence differences using coupled ligase detection and polymerase chain reactions |
| US6312892B1 (en) | 1996-07-19 | 2001-11-06 | Cornell Research Foundation, Inc. | High fidelity detection of nucleic acid differences by ligase detection reaction |
| US6770748B2 (en) | 1997-03-07 | 2004-08-03 | Takeshi Imanishi | Bicyclonucleoside and oligonucleotide analogue |
| US6794499B2 (en) | 1997-09-12 | 2004-09-21 | Exiqon A/S | Oligonucleotide analogues |
| US6027998A (en) | 1997-12-17 | 2000-02-22 | Advanced Micro Devices, Inc. | Method for fully planarized conductive line for a stack gate |
| US6506594B1 (en) | 1999-03-19 | 2003-01-14 | Cornell Res Foundation Inc | Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays |
| US6262490B1 (en) | 1999-11-05 | 2001-07-17 | Advanced Semiconductor Engineering, Inc. | Substrate strip for use in packaging semiconductor chips |
| EP1313880A2 (en) | 2000-05-30 | 2003-05-28 | PE Corporation (NY) | Methods for detecting target nucleic acids using coupled ligation and amplification |
| US6605451B1 (en) | 2000-06-06 | 2003-08-12 | Xtrana, Inc. | Methods and devices for multiplexing amplification reactions |
| AU2001290879A1 (en) | 2000-09-15 | 2002-03-26 | California Institute Of Technology | Microfabricated crossflow devices and methods |
| EP2477029A1 (en) | 2005-06-02 | 2012-07-18 | Fluidigm Corporation | Analysis using microfluidic partitioning devices |
| US9440231B2 (en) | 2007-08-14 | 2016-09-13 | Fluidigm Corporation | Polymer microfluidic biochip fabrication |
| EP2254825A4 (en) | 2008-02-22 | 2016-03-02 | Fluidigm Corp | INTEGRATED SUPPORT FOR MICROFLUIDIC DEVICE |
| WO2010009365A1 (en) | 2008-07-18 | 2010-01-21 | Raindance Technologies, Inc. | Droplet libraries |
| EP2326732A4 (en) | 2008-08-26 | 2012-11-14 | Fluidigm Corp | TEST METHODS FOR INCREASED SURPLUS OF SAMPLES AND / OR TARGETS |
| EA020593B1 (ru) | 2009-01-13 | 2014-12-30 | Флуидигм Корпорейшн | Анализ нуклеиновых кислот, полученных из единичных клеток |
| US8450063B2 (en) | 2009-01-28 | 2013-05-28 | Fluidigm Corporation | Determination of copy number differences by amplification |
| WO2010111231A1 (en) | 2009-03-23 | 2010-09-30 | Raindance Technologies, Inc. | Manipulation of microfluidic droplets |
| EP3998346A1 (en) * | 2009-03-30 | 2022-05-18 | Illumina, Inc. | Gene expression analysis in single cells |
| EP2414547B1 (en) | 2009-04-02 | 2014-03-12 | Fluidigm Corporation | Multi-primer amplification method for barcoding of target nucleic acids |
| WO2010115044A2 (en) | 2009-04-02 | 2010-10-07 | Fluidigm Corporation | Selective tagging of short nucleic acid fragments and selective protection of target sequences from degradation |
| WO2011143659A2 (en) | 2010-05-14 | 2011-11-17 | Fluidigm Corporation | Nucleic acid isolation methods |
| EP2569447A4 (en) | 2010-05-14 | 2013-11-27 | Fluidigm Corp | ASSAYS FOR THE DETECTION OF GENOTYPES, MUTATIONS OR ANEUPLOIDY |
| SG194745A1 (en) | 2011-05-20 | 2013-12-30 | Fluidigm Corp | Nucleic acid encoding reactions |
| US9304065B2 (en) * | 2012-02-29 | 2016-04-05 | Fluidigm Corporation | Methods, systems and devices for multiple single-cell capturing and processing using microfluidics |
| CN104471077B (zh) | 2012-05-21 | 2017-05-24 | 富鲁达公司 | 颗粒群的单颗粒分析 |
| US9914950B2 (en) * | 2012-08-23 | 2018-03-13 | Tufts University | Homopolymer mediated nucleic acid amplification |
| WO2014201273A1 (en) | 2013-06-12 | 2014-12-18 | The Broad Institute, Inc. | High-throughput rna-seq |
| GB201317301D0 (en) | 2013-09-30 | 2013-11-13 | Linnarsson Sten | Method for capturing and encoding nucleic acid from a plurality of single cells |
| WO2016138490A1 (en) | 2015-02-27 | 2016-09-01 | Fluidigm Corporation | Single-cell nucleic acids for high-throughput studies |
| EP3390658B1 (en) | 2015-12-16 | 2022-08-03 | Standard BioTools Inc. | High-level multiplex amplification |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2023037334A1 (en) | 2021-09-13 | 2023-03-16 | Ecole Polytechnique Federale De Lausanne (Epfl) | System and method for single cell phenotypical profiling and deterministic nanoliter-droplet encapsulation and deterministic droplet consortia assemblies |
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| CN107250445A (zh) | 2017-10-13 |
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| EP3262214B1 (en) | 2023-10-25 |
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| US20160251714A1 (en) | 2016-09-01 |
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