EP3485043A4 - Single-cell transcript sequencing - Google Patents

Single-cell transcript sequencing Download PDF

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Publication number
EP3485043A4
EP3485043A4 EP17828411.3A EP17828411A EP3485043A4 EP 3485043 A4 EP3485043 A4 EP 3485043A4 EP 17828411 A EP17828411 A EP 17828411A EP 3485043 A4 EP3485043 A4 EP 3485043A4
Authority
EP
European Patent Office
Prior art keywords
cell transcript
transcript sequencing
sequencing
cell
transcript
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.)
Withdrawn
Application number
EP17828411.3A
Other languages
German (de)
French (fr)
Other versions
EP3485043A1 (en
Inventor
Kenneth J. Livak
Richard A. Fekete
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 Corp
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 EP3485043A1 publication Critical patent/EP3485043A1/en
Publication of EP3485043A4 publication Critical patent/EP3485043A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • 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
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • 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
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Plant Pathology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
EP17828411.3A 2016-07-14 2017-07-12 Single-cell transcript sequencing Withdrawn EP3485043A4 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662362425P 2016-07-14 2016-07-14
US201762463487P 2017-02-24 2017-02-24
PCT/US2017/041770 WO2018013723A1 (en) 2016-07-14 2017-07-12 Single-cell transcript sequencing

Publications (2)

Publication Number Publication Date
EP3485043A1 EP3485043A1 (en) 2019-05-22
EP3485043A4 true EP3485043A4 (en) 2020-03-25

Family

ID=60951893

Family Applications (1)

Application Number Title Priority Date Filing Date
EP17828411.3A Withdrawn EP3485043A4 (en) 2016-07-14 2017-07-12 Single-cell transcript sequencing

Country Status (5)

Country Link
EP (1) EP3485043A4 (en)
CN (1) CN109661474A (en)
CA (1) CA3027423A1 (en)
SG (1) SG11201811048UA (en)
WO (1) WO2018013723A1 (en)

Families Citing this family (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8691509B2 (en) 2009-04-02 2014-04-08 Fluidigm Corporation Multi-primer amplification method for barcoding of target nucleic acids
SG194745A1 (en) 2011-05-20 2013-12-30 Fluidigm Corp Nucleic acid encoding reactions
US9404864B2 (en) 2013-03-13 2016-08-02 Denovo Sciences, Inc. System for imaging captured cells
CA2842359A1 (en) 2011-08-01 2013-02-07 Denovo Sciences Cell capture system and method of use
US10466160B2 (en) 2011-08-01 2019-11-05 Celsee Diagnostics, Inc. System and method for retrieving and analyzing particles
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
WO2017106777A1 (en) 2015-12-16 2017-06-22 Fluidigm Corporation High-level multiplex amplification
US10391493B2 (en) 2017-08-29 2019-08-27 Celsee Diagnostics, Inc. System and method for isolating and analyzing cells
EP3938539A4 (en) * 2019-03-12 2022-12-14 Universal Sequencing Technology Methods for single cell intracellular capture and its applications
US10633693B1 (en) 2019-04-16 2020-04-28 Celsee Diagnostics, Inc. System and method for leakage control in a particle capture system
JP7413408B2 (en) 2019-05-07 2024-01-15 バイオ－ラッド ラボラトリーズ インコーポレイテッド Systems and methods 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
SE543469C2 (en) * 2019-06-03 2021-03-02 Di Wu Method for creating a cDNA sequencing library
CA3143241A1 (en) * 2019-06-14 2020-12-17 Bio-Rad Laboratories, Inc. System and method for automated single cell processing and analyses
EP4013863A4 (en) * 2019-08-14 2023-08-30 iRepertoire, Inc. Probe-capture method for tcr alpha and beta chain vdj-recovery from oligo-dt reverse transcribed rna
US11504719B2 (en) 2020-03-12 2022-11-22 Bio-Rad Laboratories, Inc. System and method for receiving and delivering a fluid for sample processing
WO2021204860A1 (en) * 2020-04-07 2021-10-14 Trivarop Srl Device and method for determining, from a sample previously collected from an individual, that at least one target antibody has been or is present in said individual
CN115836134A (en) * 2020-06-09 2023-03-21 西姆森诊断公司 Lymphocyte clonality determination
CN114606301A (en) * 2020-12-07 2022-06-10 中国科学院脑科学与智能技术卓越创新中心 Single cell transcriptome sequencing method
GB2629157A (en) * 2023-04-18 2024-10-23 The Institute Of Cancer Res Royal Cancer Hospital T cell receptor sequencing

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060040283A1 (en) * 2001-04-11 2006-02-23 The Gov. Of The Usa As Represented By The Secretary Of The Dept. Of Health & Human Services Methods of manipulating nucleic acids
US20140308669A1 (en) * 2011-01-24 2014-10-16 Epic Science, Inc. Methods for obtaining single cells and applications of single cell omics

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8691509B2 (en) * 2009-04-02 2014-04-08 Fluidigm Corporation Multi-primer amplification method for barcoding of target nucleic acids
EP2861761A1 (en) * 2012-06-15 2015-04-22 Adaptive Biotechnologies Corporation Uniquely tagged rearranged adaptive immune receptor genes in a complex gene set
JP6558830B2 (en) * 2012-06-15 2019-08-14 ボード・オブ・リージエンツ，ザ・ユニバーシテイ・オブ・テキサス・システム High-throughput sequencing of multiple transcripts
US10590483B2 (en) * 2014-09-15 2020-03-17 Abvitro Llc High-throughput nucleotide library sequencing
US10993997B2 (en) * 2014-12-19 2021-05-04 The Broad Institute, Inc. Methods for profiling the t cell repertoire

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060040283A1 (en) * 2001-04-11 2006-02-23 The Gov. Of The Usa As Represented By The Secretary Of The Dept. Of Health & Human Services Methods of manipulating nucleic acids
US20140308669A1 (en) * 2011-01-24 2014-10-16 Epic Science, Inc. Methods for obtaining single cells and applications of single cell omics

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
ANTOINE-EMMANUEL SALIBA ET AL: "Single-cell RNA-seq: advances and future challenges", NUCLEIC ACIDS RESEARCH, vol. 42, no. 14, 22 July 2014 (2014-07-22), pages 8845 - 8860, XP055544044, ISSN: 0305-1048, DOI: 10.1093/nar/gku555 *
MOUSTAFA ATTAR ET AL: "A practical solution for preserving single cells for RNA sequencing", SCIENTIFIC REPORTS, vol. 8, no. 1, 1 February 2018 (2018-02-01), pages 2151, XP055640844, DOI: 10.1038/s41598-018-20372-7 *
See also references of WO2018013723A1 *

Also Published As

Publication number Publication date
CN109661474A (en) 2019-04-19
SG11201811048UA (en) 2019-01-30
WO2018013723A1 (en) 2018-01-18
WO2018013723A9 (en) 2019-03-28
EP3485043A1 (en) 2019-05-22
CA3027423A1 (en) 2018-01-18

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