CA2921603C - Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction - Google Patents

Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction Download PDF

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CA2921603C
CA2921603C CA2921603A CA2921603A CA2921603C CA 2921603 C CA2921603 C CA 2921603C CA 2921603 A CA2921603 A CA 2921603A CA 2921603 A CA2921603 A CA 2921603A CA 2921603 C CA2921603 C CA 2921603C
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CA2921603A1 (en
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Rickard Sandberg
Simone Picelli
Omid R. Faridani
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Ludwig Institute for Cancer Research Ltd
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    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • C12P19/30—Nucleotides
    • C12P19/34—Polynucleotides, e.g. nucleic acids, oligoribonucleotides
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Plant Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Pathology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
CA2921603A 2013-08-23 2014-08-22 Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction Active CA2921603C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201361869220P 2013-08-23 2013-08-23
US61/869,220 2013-08-23
PCT/US2014/052233 WO2015027135A1 (en) 2013-08-23 2014-08-22 Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction

Publications (2)

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CA2921603A1 CA2921603A1 (en) 2015-02-26
CA2921603C true CA2921603C (en) 2019-11-05

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US (2) US10266894B2 (enExample)
EP (1) EP3036336B1 (enExample)
JP (2) JP6336080B2 (enExample)
CN (2) CN115558661A (enExample)
CA (1) CA2921603C (enExample)
DK (1) DK3036336T3 (enExample)
ES (1) ES2827307T3 (enExample)
WO (1) WO2015027135A1 (enExample)

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* Cited by examiner, † Cited by third party
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WO2015027135A1 (en) * 2013-08-23 2015-02-26 Ludwig Institute For Cancer Research Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction
CN106460033B (zh) * 2013-12-30 2021-12-24 阿特雷卡公司 使用核酸条形码分析与单细胞缔合的核酸
EP4461812A3 (en) 2015-09-15 2025-01-22 Takara Bio USA, Inc. Method for preparing a next generation sequencing (ngs) library from a ribonucleic acid (rna) sample and compositions for practicing the same
JP7064439B2 (ja) 2015-11-04 2022-05-10 アトレカ インコーポレイテッド 単一細胞に関連する核酸の解析のための、核酸バーコードの組み合わせセット
WO2017214417A1 (en) 2016-06-10 2017-12-14 Takara Bio Usa, Inc. Methods and compositions employing blocked primers
CN106498040B (zh) * 2016-10-12 2018-10-23 浙江大学 一种分子标记微珠及基于该分子标记微珠的高通量单细胞测序方法
EP3985122A1 (en) 2016-11-10 2022-04-20 Takara Bio USA, Inc. Methods of producing amplified double stranded deoxyribonucleic acids and compositions and kits for use therein
CN110312800B (zh) 2016-11-11 2025-01-10 生物辐射实验室股份有限公司 处理核酸样本的方法
CN106868005B (zh) * 2017-03-17 2020-07-21 中山大学附属肿瘤医院 一种用于高效快速扩增cDNA末端的锚定引物及扩增方法
US11946043B2 (en) 2017-09-11 2024-04-02 Ludwig Institute For Cancer Research Ltd Selective labeling of 5-methylcytosine in circulating cell-free DNA
CN108103055B (zh) * 2018-01-09 2021-05-28 序康医疗科技（苏州）有限公司 一种单细胞rna逆转录与文库构建的方法
US11814674B2 (en) 2018-02-02 2023-11-14 The United States Of America, As Represented By The Secretary Department Of Health And Human Services Random amplification methods for extremely low input nucleic acids
WO2020036926A1 (en) 2018-08-17 2020-02-20 Cellecta, Inc. Multiplex preparation of barcoded gene specific dna fragments
WO2020136438A1 (en) 2018-12-28 2020-07-02 Biobloxx Ab Method and kit for preparing complementary dna
CN113811610A (zh) * 2019-05-09 2021-12-17 加利福尼亚太平洋生物科学股份有限公司 用于改进cDNA合成的组合物和方法
EP3998338B1 (en) 2019-07-11 2024-04-24 Tokyo University of Science Foundation Method for amplifying nucleic acid using solid-phase carrier
WO2021236963A1 (en) * 2020-05-20 2021-11-25 Chan Zuckerberg Biohub, Inc. Total rna profiling of biological samples and single cells
WO2023241721A1 (zh) * 2022-06-17 2023-12-21 复旦大学 基于拓扑捕获的rna样本处理系统
WO2024185884A1 (ja) 2023-03-09 2024-09-12 イムノジェネテクス株式会社 相補ｄｎａ鎖を増幅する方法
CN116497105B (zh) * 2023-06-28 2023-09-29 浙江大学 基于末端转移酶的单细胞转录组测序试剂盒及测序方法
CN119776495A (zh) * 2024-12-31 2025-04-08 北京普译生物科技有限公司 一种cDNA建库中的模板转换方法

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US5962271A (en) 1996-01-03 1999-10-05 Cloutech Laboratories, Inc. Methods and compositions for generating full-length cDNA having arbitrary nucleotide sequence at the 3'-end
JP4975905B2 (ja) 1999-03-18 2012-07-11 エクシコン エ／エス 複合生物試料における核酸の単工程調製及び検出
ES2706227T3 (es) 2009-03-30 2019-03-27 Illumina Inc Análisis de expresión génica en células individuales
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JP6017458B2 (ja) 2011-02-02 2016-11-02 ユニヴァーシティ・オブ・ワシントン・スルー・イッツ・センター・フォー・コマーシャリゼーション 大量並列連続性マッピング
US9260753B2 (en) * 2011-03-24 2016-02-16 President And Fellows Of Harvard College Single cell nucleic acid detection and analysis
WO2015027135A1 (en) * 2013-08-23 2015-02-26 Ludwig Institute For Cancer Research Methods and compositions for cdna synthesis and single-cell transcriptome profiling using template switching reaction

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Publication number Publication date
US20190264284A1 (en) 2019-08-29
JP2018088924A (ja) 2018-06-14
DK3036336T3 (da) 2020-11-02
EP3036336A4 (en) 2017-06-28
CA2921603A1 (en) 2015-02-26
JP6603699B2 (ja) 2019-11-06
CN105579587A (zh) 2016-05-11
ES2827307T3 (es) 2021-05-20
EP3036336B1 (en) 2020-09-30
CN115558661A (zh) 2023-01-03
US10266894B2 (en) 2019-04-23
EP3036336A1 (en) 2016-06-29
US20160258016A1 (en) 2016-09-08
JP2016527919A (ja) 2016-09-15
WO2015027135A1 (en) 2015-02-26
JP6336080B2 (ja) 2018-06-06

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