CA2976681A1 - Single-cell nucleic acids for high-throughput studies - Google Patents

Single-cell nucleic acids for high-throughput studies Download PDF

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Publication number
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
Authority
CA
Canada
Prior art keywords
linker
barcode
primer
umi
capture
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CA2976681A
Other languages
English (en)
French (fr)
Inventor
Carolyn G. Conant
Tze Howe Charn
Jason A. A. West
Xiaohui Wang
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Standard Biotools Inc
Original Assignee
Fluidigm Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Fluidigm Corp filed Critical Fluidigm Corp
Publication of CA2976681A1 publication Critical patent/CA2976681A1/en
Pending legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • C12Q1/6874Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027Containers 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
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027Containers 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
    • B01L3/502761Containers 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
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06Fluid handling related problems
    • B01L2200/0647Handling flowable solids, e.g. microscopic beads, cells, particles
    • B01L2200/0652Sorting or classification of particles or molecules
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/06Auxiliary integrated devices, integrated components
    • B01L2300/0609Holders integrated in container to position an object
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0893Geometry, 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)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Dispersion Chemistry (AREA)
  • Clinical Laboratory Science (AREA)
  • Hematology (AREA)
  • Fluid Mechanics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA2976681A 2015-02-27 2016-02-26 Single-cell nucleic acids for high-throughput studies Pending CA2976681A1 (en)

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 (OSRAM)
EP (1) EP3262214B1 (OSRAM)
JP (1) JP2018509896A (OSRAM)
CN (1) CN107250445A (OSRAM)
CA (1) CA2976681A1 (OSRAM)
SG (1) SG11201706636PA (OSRAM)
WO (1) WO2016138490A1 (OSRAM)

Cited By (1)

* Cited by examiner, † Cited by third party
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)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SG174617A1 (en) 2009-04-02 2011-10-28 Fluidigm Corp 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
EP2710172B1 (en) 2011-05-20 2017-03-29 Fluidigm Corporation Nucleic acid encoding reactions
US9404864B2 (en) 2013-03-13 2016-08-02 Denovo Sciences, Inc. System for imaging captured cells
US10466160B2 (en) 2011-08-01 2019-11-05 Celsee Diagnostics, Inc. System and method for retrieving and analyzing particles
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
US10391490B2 (en) 2013-05-31 2019-08-27 Celsee Diagnostics, Inc. System and method for isolating and analyzing cells
US9856535B2 (en) 2013-05-31 2018-01-02 Denovo Sciences, Inc. System for isolating cells
CA2976681A1 (en) 2015-02-27 2016-09-01 Fluidigm Corporation Single-cell nucleic acids for high-throughput studies
SG11201803646YA (en) 2015-11-04 2018-05-30 Atreca Inc Combinatorial sets of nucleic acid barcodes for analysis of nucleic acids associated with single cells
CA3006994A1 (en) 2015-12-16 2017-06-22 Fluidigm Corporation High-level multiplex amplification
US10202641B2 (en) 2016-05-31 2019-02-12 Cellular Research, Inc. Error correction in amplification of samples
WO2018081113A1 (en) 2016-10-24 2018-05-03 Sawaya Sterling Concealing information present within nucleic acids
US11753743B2 (en) 2017-02-13 2023-09-12 Yale University High-throughput single-cell polyomics
AU2018281745B2 (en) 2017-06-05 2022-05-19 Becton, Dickinson And Company Sample indexing for single cells
KR102683229B1 (ko) * 2017-06-20 2024-07-08 소마젠 인크 고유 분자 식별자를 갖는 라이브러리 제조 방법 및 시스템
AU2018323449B2 (en) 2017-08-29 2020-09-03 Bio-Rad Laboratories, Inc. System and method for isolating and analyzing cells
US20200347441A1 (en) * 2017-08-30 2020-11-05 Kapa Biosystems, Inc. Transposase compositions, methods of making, and methods of screening
US20210087549A1 (en) * 2018-02-23 2021-03-25 Yale University Single-cell freeze-thaw lysis
ES2945191T3 (es) 2018-05-03 2023-06-29 Becton Dickinson Co Análisis de muestras multiómicas de alto rendimiento
EP3837380A4 (en) * 2018-08-17 2022-05-11 Cellecta, Inc. MULTIPLEX PREPARATION OF BARCODE GENE-SPECIFIC DNA FRAGMENTS
EP4471156A3 (en) * 2018-10-01 2025-02-26 Becton, Dickinson and Company Determining 5' transcript sequences
EP3924506A1 (en) 2019-02-14 2021-12-22 Becton Dickinson and Company Hybrid targeted and whole transcriptome amplification
US10633693B1 (en) 2019-04-16 2020-04-28 Celsee Diagnostics, Inc. System and method for leakage control in a particle capture system
SG11202112151UA (en) 2019-05-07 2021-12-30 Bio Rad Laboratories System and method for automated single cell processing
US11273439B2 (en) 2019-05-07 2022-03-15 Bio-Rad Laboratories, Inc. System and method for target material retrieval from microwells
KR20250084977A (ko) 2019-06-14 2025-06-11 바이오 래드 래버러토리스 인코오포레이티드 자동화된 단일 세포 처리 및 분석을 위한 시스템 및 방법
EP4010494A1 (en) * 2019-08-08 2022-06-15 INSERM (Institut National de la Santé et de la Recherche Médicale) Rna sequencing method for the analysis of b and t cell transcriptome in phenotypically defined b and t cell subsets
EP4025709A1 (en) * 2019-09-06 2022-07-13 10X Genomics, Inc. Systems and methods for barcoding cells and cell beads
CN114555824A (zh) * 2019-10-11 2022-05-27 布莱克霍克基因组学有限责任公司 使用长读测序鉴定基因组结构变体
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
EP4471155A3 (en) 2020-01-29 2024-12-18 Becton, Dickinson and Company Barcoded wells for spatial mapping of single cells through sequencing
CN115151810A (zh) 2020-02-25 2022-10-04 贝克顿迪金森公司 实现使用单细胞样品作为单色补偿对照的双特异性探针
US11504719B2 (en) 2020-03-12 2022-11-22 Bio-Rad Laboratories, Inc. System and method for receiving and delivering a fluid for sample processing
CN115605614A (zh) 2020-05-14 2023-01-13 贝克顿迪金森公司(Us) 用于免疫组库谱分析的引物
US12157913B2 (en) 2020-06-02 2024-12-03 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
JP2023547732A (ja) * 2020-11-03 2023-11-13 エイシーティ・ジェノミックス(アイピー)リミテッド 遺伝子改変を検出するための標的化シークエンシング方法およびそのキット
US12392771B2 (en) 2020-12-15 2025-08-19 Becton, Dickinson And Company Single cell secretome analysis
CN118369438A (zh) 2021-12-10 2024-07-19 伯乐实验室有限公司 用形态可调节功能化颗粒进行样品处理的组合物、方法和系统

Family Cites Families (34)

* Cited by examiner, † Cited by third party
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
EP2574617B1 (en) 1996-02-09 2016-04-20 Cornell Research Foundation, Inc. Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays
WO1997045559A1 (en) 1996-05-29 1997-12-04 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
EP2299256A3 (en) 2000-09-15 2012-10-10 California Institute Of Technology Microfabricated crossflow devices and methods
EP2477029A1 (en) 2005-06-02 2012-07-18 Fluidigm Corporation Analysis using microfluidic partitioning devices
WO2009023547A2 (en) 2007-08-14 2009-02-19 Arcxis Biotechnologies Polymer microfluidic biochip fabrication
CN102015522B (zh) 2008-02-22 2013-07-03 弗卢迪格姆公司 用于微流体器件的集成载体
WO2010009365A1 (en) 2008-07-18 2010-01-21 Raindance Technologies, Inc. Droplet libraries
CN102203287B (zh) 2008-08-26 2017-09-19 弗卢迪格姆公司 增加样本和/或靶通量的测定方法
CN102348811A (zh) 2009-01-13 2012-02-08 弗卢伊蒂格姆公司 单细胞核酸分析
WO2010088288A2 (en) 2009-01-28 2010-08-05 Fluidigm Corporation Determination of copy number differences by amplification
US8528589B2 (en) 2009-03-23 2013-09-10 Raindance Technologies, Inc. Manipulation of microfluidic droplets
EP3998346A1 (en) 2009-03-30 2022-05-18 Illumina, Inc. Gene expression analysis in single cells
SG174617A1 (en) 2009-04-02 2011-10-28 Fluidigm Corp Multi-primer amplification method for barcoding of target nucleic acids
US20100285537A1 (en) 2009-04-02 2010-11-11 Fluidigm Corporation Selective tagging of short nucleic acid fragments and selective protection of target sequences from degradation
EP2569453B1 (en) 2010-05-14 2015-12-16 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
EP2710172B1 (en) * 2011-05-20 2017-03-29 Fluidigm Corporation Nucleic acid encoding reactions
EP3627140A1 (en) * 2012-02-29 2020-03-25 Fluidigm Corporation Methods, systems, and devices for multiple single-cell capturing and processing using microfluidics
CA2874343C (en) 2012-05-21 2021-11-09 Fluidigm Corporation Single-particle analysis of particle populations
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
CA2976681A1 (en) 2015-02-27 2016-09-01 Fluidigm Corporation Single-cell nucleic acids for high-throughput studies
CA3006994A1 (en) 2015-12-16 2017-06-22 Fluidigm Corporation High-level multiplex amplification

Cited By (1)

* Cited by examiner, † Cited by third party
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

Also Published As

Publication number Publication date
EP3262214B1 (en) 2023-10-25
US10954560B2 (en) 2021-03-23
US20190185929A1 (en) 2019-06-20
SG11201706636PA (en) 2017-09-28
WO2016138490A1 (en) 2016-09-01
US20160251714A1 (en) 2016-09-01
US10190163B2 (en) 2019-01-29
CN107250445A (zh) 2017-10-13
EP3262214A4 (en) 2018-07-25
EP3262214A1 (en) 2018-01-03
JP2018509896A (ja) 2018-04-12

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