CA2907493A1 - Multiplex labeling of molecules by sequential hybridization barcoding - Google Patents

Multiplex labeling of molecules by sequential hybridization barcoding

Info

Publication number
CA2907493A1
CA2907493A1 CA2907493A CA2907493A CA2907493A1 CA 2907493 A1 CA2907493 A1 CA 2907493A1 CA 2907493 A CA2907493 A CA 2907493A CA 2907493 A CA2907493 A CA 2907493A CA 2907493 A1 CA2907493 A1 CA 2907493A1
Authority
CA
Canada
Prior art keywords
oligonucleotide
oligonucleotides
detectably labeled
labeled
detectable moiety
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
CA2907493A
Other languages
English (en)
French (fr)
Inventor
Long Cai
Eric Lubeck
Timur Zhiyentayev
Ahmet COSKUN
Ting-Fang HE
Chang Ho Sohn
Sheel SHAH
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.)
California Institute of Technology
Original Assignee
California Institute of Technology
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=51867841&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=CA2907493(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by California Institute of Technology filed Critical California Institute of Technology
Publication of CA2907493A1 publication Critical patent/CA2907493A1/en
Pending legal-status Critical Current

Links

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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6841—In situ hybridisation
    • 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
    • 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
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N15/14—Optical investigation techniques, e.g. flow cytometry
    • G01N15/1429—Signal processing
    • G01N15/1433—Signal processing using image recognition
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/6456—Spatial resolved fluorescence measurements; Imaging
    • G01N21/6458—Fluorescence microscopy
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/06—Means for illuminating specimens
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/16—Microscopes adapted for ultraviolet illumination ; Fluorescence microscopes
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/34—Microscope slides, e.g. mounting specimens on microscope slides
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/107—Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1006—Investigating individual particles for cytology
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2201/00—Features of devices classified in G01N21/00
    • G01N2201/06—Illumination; Optics
    • G01N2201/068—Optics, miscellaneous
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2201/00—Features of devices classified in G01N21/00
    • G01N2201/10—Scanning

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • General Physics & Mathematics (AREA)
  • Optics & Photonics (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Signal Processing (AREA)
  • Dispersion Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Microscoopes, Condenser (AREA)
  • Computer Vision & Pattern Recognition (AREA)
CA2907493A 2013-04-30 2014-04-30 Multiplex labeling of molecules by sequential hybridization barcoding Pending CA2907493A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201361817651P 2013-04-30 2013-04-30
US61/817,651 2013-04-30
US201461971974P 2014-03-28 2014-03-28
US61/971,974 2014-03-28
PCT/US2014/036258 WO2014182528A2 (en) 2013-04-30 2014-04-30 Multiplex labeling of molecules by sequential hybridization barcoding

Publications (1)

Publication Number Publication Date
CA2907493A1 true CA2907493A1 (en) 2014-11-13

Family

ID=51867841

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2907493A Pending CA2907493A1 (en) 2013-04-30 2014-04-30 Multiplex labeling of molecules by sequential hybridization barcoding

Country Status (9)

Country Link
US (6) US10457980B2 (enExample)
EP (2) EP3626833A1 (enExample)
JP (3) JP6605452B2 (enExample)
KR (2) KR102368591B1 (enExample)
CN (2) CN110669826B (enExample)
CA (1) CA2907493A1 (enExample)
DK (1) DK2992115T4 (enExample)
FI (1) FI2992115T4 (enExample)
WO (1) WO2014182528A2 (enExample)

Families Citing this family (135)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DK2633071T3 (en) 2010-10-27 2017-01-30 Harvard College COMPOSITIONS OF "MAINTENANCE" PRIMER DUPLEXES AND METHODS OF USE
JP2014531908A (ja) 2011-10-14 2014-12-04 プレジデント アンド フェローズ オブ ハーバード カレッジ 構造アッセンブリによる配列決定
ES2952728T3 (es) 2011-12-22 2023-11-03 Harvard College Métodos para la detección de analitos
ES2991004T3 (es) 2011-12-22 2024-12-02 Harvard College Métodos para la detección de analitos
WO2013184754A2 (en) 2012-06-05 2013-12-12 President And Fellows Of Harvard College Spatial sequencing of nucleic acids using dna origami probes
EP4163617A1 (en) 2012-08-09 2023-04-12 The Board of Trustees of the Leland Stanford Junior University Methods and compositions for preparing biological specimens for microscopic analysis
DK3511423T4 (da) 2012-10-17 2024-07-29 Spatial Transcriptomics Ab Fremgangsmåder og produkt til optimering af lokaliseret eller rumlig detektion af genekspression i en vævsprøve
CA2891939C (en) 2012-11-19 2020-10-27 Apton Biosystems, Inc. Digital analysis of molecular analytes using single molecule detection
US10829816B2 (en) 2012-11-19 2020-11-10 Apton Biosystems, Inc. Methods of analyte detection
US10138509B2 (en) 2013-03-12 2018-11-27 President And Fellows Of Harvard College Method for generating a three-dimensional nucleic acid containing matrix
US10510435B2 (en) 2013-04-30 2019-12-17 California Institute Of Technology Error correction of multiplex imaging analysis by sequential hybridization
CN110669826B (zh) * 2013-04-30 2025-01-07 加州理工学院 通过顺序杂交编条形码的分子多重标记
RU2690935C2 (ru) 2013-06-04 2019-06-06 Президент Энд Фэллоуз Оф Харвард Коллидж Направляемая рнк регуляция транскрипции
EP4234716A3 (en) 2013-06-25 2023-12-06 Prognosys Biosciences, Inc. Methods for determining spatial patterns of biological targets in a sample
CA2947898A1 (en) 2014-05-30 2015-12-03 The Board Of Trustees Of The Leland Stanford Junior University Methods and devices for imaging large intact tissue samples
WO2016007839A1 (en) 2014-07-11 2016-01-14 President And Fellows Of Harvard College Methods for high-throughput labelling and detection of biological features in situ using microscopy
ES3014093T3 (en) 2014-07-30 2025-04-16 Harvard College Method for determining nucleic acids
US10900065B2 (en) 2014-11-14 2021-01-26 University Of Washington Methods and kits for labeling cellular molecules
EP4119677B1 (en) 2015-04-10 2023-06-28 Spatial Transcriptomics AB Spatially distinguished, multiplex nucleic acid analysis of biological specimens
SG10202107055SA (en) 2015-07-17 2021-08-30 Nanostring Technologies Inc Simultaneous quantification of a plurality of proteins in a user-defined region of a cross-sectioned tissue
JP6882282B2 (ja) 2015-11-03 2021-06-02 プレジデント アンド フェローズ オブ ハーバード カレッジ 三次元核酸含有マトリックスの立体撮像のための方法と装置
US11254974B2 (en) 2016-02-10 2022-02-22 The Board Of Trustees Of The Leland Stanford Junior University RNA fixation and detection in clarity-based hydrogel tissue
EP4613756A3 (en) 2016-04-25 2025-11-12 President And Fellows Of Harvard College Hybridization chain reaction methods for in situ molecular detection
WO2017196527A1 (en) * 2016-05-10 2017-11-16 Arizona Board Of Regents On Behalf Of Arizona State University Consecutive hybridization for multiplexed analysis of biological samples
US11269171B2 (en) * 2016-05-19 2022-03-08 Huron Technologies International Inc. Spectrally-resolved scanning microscope
WO2017222453A1 (en) 2016-06-21 2017-12-28 Hauling Thomas Nucleic acid sequencing
CN116064727A (zh) * 2016-07-27 2023-05-05 斯坦福大学托管董事会 高度复用荧光成像
CN109804084A (zh) * 2016-08-01 2019-05-24 加州理工学院 基于具有嵌入纠错机制的伪彩色条形码的分子靶的顺序探测
US12421540B2 (en) 2016-08-01 2025-09-23 California Institute Of Technology Sequential probing of molecular targets based on pseudo-color barcodes with embedded error correction mechanism
CN109923216B (zh) 2016-08-31 2024-08-02 哈佛学院董事及会员团体 将生物分子的检测组合到使用荧光原位测序的单个试验的方法
EP3507364A4 (en) 2016-08-31 2020-05-20 President and Fellows of Harvard College METHODS OF GENERATING NUCLEIC ACID SEQUENCE LIBRARIES FOR IN SITU FLUORESCENT SEQUENCING DETECTION
EP3299472A1 (en) * 2016-09-27 2018-03-28 Deutsches Krebsforschungszentrum Stiftung des Öffentlichen Rechts Method for labeling oligonucleotide probes
WO2018064640A1 (en) * 2016-10-01 2018-04-05 Berkeley Lights, Inc. Dna barcode compositions and methods of in situ identification in a microfluidic device
US11352660B2 (en) * 2016-10-04 2022-06-07 Howard Hughes Medical Institute Materials and methods for serial multiplexed detection of RNA in cells and tissues
JP6730525B2 (ja) 2016-11-21 2020-07-29 ナノストリング テクノロジーズ，インコーポレイティド 化学組成物とそれを利用する方法
AU2017370751B2 (en) * 2016-12-09 2023-11-09 Ultivue, Inc. Improved methods for multiplex imaging using labeled nucleic acid imaging agents
EP3568492B1 (en) * 2017-01-10 2025-01-01 President and Fellows of Harvard College Multiplexed signal amplification
CN114921537A (zh) 2017-03-17 2022-08-19 雅普顿生物系统公司 测序和高分辨率成像
US11185568B2 (en) 2017-04-14 2021-11-30 President And Fellows Of Harvard College Methods for generation of cell-derived microfilament network
US11788123B2 (en) 2017-05-26 2023-10-17 President And Fellows Of Harvard College Systems and methods for high-throughput image-based screening
US20200217850A1 (en) * 2017-09-15 2020-07-09 Apton Biosystems, Inc. Heterogeneous single cell profiling using molecular barcoding
CN118599963A (zh) 2017-09-22 2024-09-06 华盛顿大学 细胞分子的原位组合标记
CN120210336A (zh) 2017-10-06 2025-06-27 10X基因组学有限公司 Rna模板化连接
WO2019075091A1 (en) * 2017-10-11 2019-04-18 Expansion Technologies MULTIPLEXED IN SITU HYBRIDIZATION OF TISSUE SECTIONS FOR SPATIALLY RESOLVED TRANSCRIPTOMIC WITH EXPANSION MICROSCOPY
WO2019103996A1 (en) 2017-11-21 2019-05-31 Expansion Technologies Expansion microscopy compatible and multiplexed in situ hybridization of formalin fixed paraffin embedded tissue sections for spatially resolved transcriptomics
EP3720972A1 (en) * 2017-12-08 2020-10-14 California Institute of Technology Multiplex labeling of molecules by sequential hybridization barcoding with rapid switching and rehybridzation of probes
EP3743525A4 (en) 2018-01-26 2021-09-29 President and Fellows of Harvard College PROXIMITY DETECTION METHODS AND COMPOSITIONS
KR20250161650A (ko) * 2018-02-12 2025-11-17 브루커 스페이셜 바이올로지, 인크. 유전자 및 단백질 발현을 검출하는 생체 분자 프로브 및 방법
EP3794146B1 (en) 2018-05-14 2025-12-10 Bruker Spatial Biology, Inc. Method for identifying a predetermined nucleotide sequence
CN112770776B (zh) 2018-07-30 2025-08-19 瑞德库尔有限责任公司 用于样品处理或分析的方法和系统
WO2020061237A1 (en) 2018-09-19 2020-03-26 Apton Biosystems, Inc. Densely-packed analyte layers and detection methods
WO2020076976A1 (en) 2018-10-10 2020-04-16 Readcoor, Inc. Three-dimensional spatial molecular indexing
WO2020093019A2 (en) 2018-11-01 2020-05-07 California Institute Of Technology A multi-channel line scanner for fast large field and confocal imaging
WO2020117713A1 (en) * 2018-12-03 2020-06-11 California Institute Of Technology In situ readout of dna barcodes
CN113366116A (zh) 2018-12-13 2021-09-07 哈佛学院院长及董事 用于merfish和其他应用的扩增方法和系统
KR20210104030A (ko) 2018-12-14 2021-08-24 얼티뷰, 인크. 표적을 순차적으로 검출하는 방법 및 조성물
WO2020214642A1 (en) * 2019-04-19 2020-10-22 Becton, Dickinson And Company Methods of associating phenotypical data and single cell sequencing data
CN113906147B (zh) 2019-05-31 2024-09-13 10X基因组学有限公司 检测目标核酸分子的方法
CN110484440A (zh) * 2019-08-30 2019-11-22 希格诺(南京)生物科技有限公司 一种核酸荧光原位检测装置及方法
US12163189B2 (en) 2019-11-27 2024-12-10 University Of Washington Method for preparation and high-throughput microbial single-cell RNA sequencing of bacteria
CN115066501A (zh) * 2019-12-19 2022-09-16 阿科亚生物科学股份有限公司 Rna检测
GB201919032D0 (en) 2019-12-20 2020-02-05 Cartana Ab Method of detecting an analyte
US12110548B2 (en) 2020-02-03 2024-10-08 10X Genomics, Inc. Bi-directional in situ analysis
US12215379B2 (en) 2020-02-17 2025-02-04 10X Genomics, Inc. In situ analysis of chromatin interaction
CN115917007A (zh) * 2020-02-18 2023-04-04 新加坡科技研究局 核酸探针
JP2023514749A (ja) 2020-02-21 2023-04-07 １０エックス ジェノミクス インコーポレイテッド 統合型インサイチュ空間的アッセイのための方法および組成物
US12188085B2 (en) 2020-03-05 2025-01-07 10X Genomics, Inc. Three-dimensional spatial transcriptomics with sequencing readout
US12209273B2 (en) 2020-06-12 2025-01-28 10X Genomics, Inc. Nucleic acid assays using click chemistry bioconjugation
JP2023529682A (ja) 2020-06-18 2023-07-11 リゾルブ バイオサイエンシズ ゲゼルシャフト ミット ベシュレンクテル ハフツング 試料中の異なる分析物を検出するための多重的方法
US20220042097A1 (en) * 2020-08-04 2022-02-10 The Broad Institute, Inc. In-situ spatial transcriptomics and proteomics
US12297499B2 (en) 2020-08-17 2025-05-13 10X Genomics, Inc. Multicomponent nucleic acid probes for sample analysis
US20220049303A1 (en) 2020-08-17 2022-02-17 Readcoor, Llc Methods and systems for spatial mapping of genetic variants
US20220083832A1 (en) 2020-09-16 2022-03-17 10X Genomics, Inc. Methods and systems for barcode-assisted image registration and alignment
US12071667B2 (en) 2020-11-04 2024-08-27 10X Genomics, Inc. Sequence analysis using meta-stable nucleic acid molecules
EP4247978A1 (en) 2020-11-18 2023-09-27 10X Genomics, Inc. Methods and compositions for analyzing immune infiltration in cancer stroma to predict clinical outcome
US11333588B1 (en) 2020-12-07 2022-05-17 Nebulum Technologies Co., Ltd. Matrix-assisted methods and compositions to prepare biological samples for super-resolution imaging
EP4012046A1 (en) 2020-12-11 2022-06-15 10X Genomics, Inc. Methods and compositions for multimodal in situ analysis
US12060603B2 (en) 2021-01-19 2024-08-13 10X Genomics, Inc. Methods for internally controlled in situ assays using padlock probes
WO2022164809A1 (en) 2021-01-26 2022-08-04 10X Genomics, Inc. Nucleic acid analog probes for in situ analysis
US12275984B2 (en) 2021-03-02 2025-04-15 10X Genomics, Inc. Sequential hybridization and quenching
WO2022187366A1 (en) 2021-03-03 2022-09-09 10X Genomics, Inc. Analyte detection in situ using nucleic acid origami
US20240247302A1 (en) 2021-05-28 2024-07-25 California Institute Of Technology Massive generation of chemically ligateable probes for multiplexed fish
CN117396613A (zh) 2021-06-01 2024-01-12 10X基因组学有限公司 用于分析物检测和探针解析的方法和组合物
EP4347880A1 (en) 2021-06-02 2024-04-10 10X Genomics, Inc. Sample analysis using asymmetric circularizable probes
CN118265800A (zh) 2021-06-08 2024-06-28 加州理工学院 用于多路fish的比率计量符号与顺序编码
CN117651855A (zh) 2021-07-13 2024-03-05 10X基因组学有限公司 用于制备具有可控厚度的聚合基质的方法
WO2023009842A1 (en) 2021-07-30 2023-02-02 10X Genomics, Inc. Methods and compositions for synchronizing reactions in situ
US12139751B2 (en) 2021-07-30 2024-11-12 10X Genomics, Inc. Circularizable probes for in situ analysis
US12460251B2 (en) 2021-08-03 2025-11-04 10X Genomics, Inc. Stabilization and/or compaction of nucleic acid molecules
US12391984B2 (en) 2021-08-03 2025-08-19 10X Genomics, Inc. Compositions and methods for rolling circle amplification
CN118043476A (zh) 2021-08-03 2024-05-14 10X基因组学有限公司 核酸多联体及其稳定和/或压缩方法
JP2024528255A (ja) 2021-08-06 2024-07-26 リゾルブ バイオサイエンシズ ゲーエムベーハー 病原体含有試料中の分析物の検出方法
CN117858958A (zh) 2021-08-16 2024-04-09 10X基因组学有限公司 包含分割条形码区的探针和使用方法
AU2022374388A1 (en) 2021-10-25 2024-03-21 Resolve Biosciences Gmbh Method of mounting a biological sample on a surface
WO2023102118A2 (en) 2021-12-01 2023-06-08 10X Genomics, Inc. Methods, compositions, and systems for improved in situ detection of analytes and spatial analysis
EP4453247A1 (en) * 2021-12-23 2024-10-30 California Institute of Technology Suppression of non-specific signals by exonucleases in fish experiment
EP4423296A2 (en) 2021-12-27 2024-09-04 10X Genomics, Inc. Methods and compositions for rolling circle amplification
EP4466376A1 (en) 2022-01-21 2024-11-27 10X Genomics, Inc. Multiple readout signals for analyzing a sample
CN118974836A (zh) 2022-03-08 2024-11-15 10X基因组学有限公司 将光学拥挤最小化的原位代码设计方法
EP4505177A1 (en) 2022-04-01 2025-02-12 10x Genomics, Inc. Compositions and methods for targeted masking of autofluorescence
EP4504969A1 (en) 2022-04-06 2025-02-12 10X Genomics, Inc. Methods for multiplex cell analysis
CN119213143A (zh) 2022-05-11 2024-12-27 10X基因组学有限公司 用于原位测序的组合物和方法
WO2023245190A1 (en) 2022-06-17 2023-12-21 10X Genomics, Inc. Catalytic de-crosslinking of samples for in situ analysis
WO2024002726A1 (en) * 2022-06-30 2024-01-04 Resolve Biosciences Gmbh High resolution multiplex method for detecting at least two targets with a distance of beyond the diffraction limit in a sample
CN119301155A (zh) 2022-07-19 2025-01-10 百进生物科技公司 抗cd157抗体、其抗原结合片段和组合物及其制备和使用方法
US20240101978A1 (en) 2022-08-12 2024-03-28 10X Genomics, Inc. Puma1 polymerases and uses thereof
WO2024040060A1 (en) 2022-08-16 2024-02-22 10X Genomics, Inc. Ap50 polymerases and uses thereof
CN119968395A (zh) 2022-08-18 2025-05-09 百进生物科技公司 抗axl抗体、其抗原结合片段及其制备和使用方法
EP4602344A1 (en) 2022-10-14 2025-08-20 10X Genomics, Inc. Methods for analysis of biological samples
US20240167081A1 (en) 2022-11-08 2024-05-23 10X Genomics,Inc. Immobilization methods and compositions for in situ detection
WO2024107727A1 (en) 2022-11-18 2024-05-23 10X Genomics, Inc. Systems and methods for actively mitigating vibrations
DE102022131447A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131441A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131442A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Zuordnen von Bildbereichen einer Bildfolge zu Ergebnisklassen mittels eines Analytdaten-Auswertesystems mit einem Verarbeitungsmodells
DE102022131445A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131451A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Bestimmen einer Signal-Zusammensetzung von Signalfolgen einer Bildfolge
DE102022131444A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren zum Identifizieren von Analyten in einer Bildfolge
DE102022131449A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131448A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131450A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
DE102022131446A1 (de) 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Aufbereiten von Daten zum Identifizieren von Analyten
EP4634404A1 (en) 2022-12-16 2025-10-22 10X Genomics, Inc. Methods and compositions for assessing performance
WO2024167925A1 (en) * 2023-02-06 2024-08-15 Applied Materials, Inc. Convolutional neural network model for imaging via fluorescence in situ hybridization
WO2024215715A2 (en) * 2023-04-11 2024-10-17 President And Fellows Of Harvard College Chemical ligation techniques
WO2024243217A1 (en) 2023-05-25 2024-11-28 BioLegend, Inc. Ceacam6 binding antibodies and antigen-binding fragments thereof
WO2024254071A1 (en) * 2023-06-05 2024-12-12 President And Fellows Of Harvard College Three-dimensional imaging systems and methods for determining nucleic acids in thick tissues
US12319956B2 (en) 2023-07-31 2025-06-03 10X Genomics, Inc. Methods and systems for targeted RNA cleavage and target RNA-primed rolling circle amplification
DE102023122213A1 (de) 2023-08-18 2025-02-20 Carl Zeiss Microscopy Gmbh Verfahren zum Bereitstellen von Quelldaten zum Trainieren oder Validieren eines Verarbeitungsmodells zum Verarbeiten von Analyt-Bildfolgen
WO2025072313A1 (en) 2023-09-27 2025-04-03 BioLegend, Inc. Anti-gpc4 antibodies
WO2025093690A1 (en) 2023-11-02 2025-05-08 Resolve Biosciences Gmbh Method for preparing tissue sections
WO2025099313A1 (en) 2023-11-10 2025-05-15 Resolve Biosciences Gmbh Reducing background fluorescence in single molecule fluorescence in situ hybridization applications
WO2025125442A1 (en) 2023-12-13 2025-06-19 Resolve Biosciences Gmbh High resolution multiplex method for detecting at least two targets
WO2025132546A1 (en) 2023-12-19 2025-06-26 Resolve Biosciences Gmbh Method for reducing nonspecific signals in in-situ hybridization assays
WO2025194033A1 (en) 2024-03-15 2025-09-18 10X Genomics, Inc. Systems and methods for covering and sealing an open well
DE102024116989A1 (de) * 2024-06-17 2025-12-18 Carl Zeiss Microscopy Gmbh Verfahren und Vorrichtung zum Bestimmen eines Konfidenzmaßes beim Auswerten von Analyt-Bilddaten einer Probe

Family Cites Families (61)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA1228811A (en) 1983-05-05 1987-11-03 Robert G. Pergolizzi Assay method utilizing polynucleotide sequences
US5367066A (en) 1984-10-16 1994-11-22 Chiron Corporation Oligonucleotides with selectably cleavable and/or abasic sites
US6280929B1 (en) * 1986-01-16 2001-08-28 The Regents Of The University Of California Method of detecting genetic translocations identified with chromosomal abnormalities
CA1317860C (en) 1987-04-01 1993-05-18 Daniel Louis Kacian Techniques for preparing specimens for bacterial assays
US5424413A (en) * 1992-01-22 1995-06-13 Gen-Probe Incorporated Branched nucleic acid probes
US5629147A (en) * 1992-07-17 1997-05-13 Aprogenex, Inc. Enriching and identifying fetal cells in maternal blood for in situ hybridization
US5955272A (en) * 1993-02-26 1999-09-21 University Of Massachusetts Detection of individual gene transcription and splicing
US20030017081A1 (en) * 1994-02-10 2003-01-23 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
US5681702A (en) 1994-08-30 1997-10-28 Chiron Corporation Reduction of nonspecific hybridization by using novel base-pairing schemes
US5866331A (en) * 1995-10-20 1999-02-02 University Of Massachusetts Single molecule detection by in situ hybridization
US6194146B1 (en) * 1997-06-13 2001-02-27 Bioseparations, Inc. Situ and in vitro hybridization method and buffer
JP3517642B2 (ja) * 1998-03-18 2004-04-12 ロシュ ダイアグノスティックス ゲーエムベーハー アポトーシス産物の検出
JP3267576B2 (ja) 1998-11-09 2002-03-18 三光純薬株式会社 プローブ高分子の形成方法
JP2003527075A (ja) * 1999-03-25 2003-09-16 ハイセック，インコーポレーテッド ハイブリダイゼーションによる配列分析のための、溶液ベースの方法
US20060275782A1 (en) 1999-04-20 2006-12-07 Illumina, Inc. Detection of nucleic acid reactions on bead arrays
US6534266B1 (en) * 1999-04-22 2003-03-18 Albert Einstein College Of Medicine Of Yeshiva University Assay of transcription sites by multi-fluor fish
ES2287134T3 (es) 2000-06-02 2007-12-16 Bayer Corporation Procedimiento para la deteccion y localizacion de genes in situ usando hibridacion de adn ramificado.
JP4537053B2 (ja) * 2001-06-25 2010-09-01 ジョージア テック リサーチ コーポレーション 二重共鳴エネルギー転移核酸プローブ
WO2003016574A1 (en) * 2001-08-16 2003-02-27 Zhifeng Shao Analysis of gene expression profiles using sequential hybridization
CA2458802C (en) * 2001-09-06 2016-06-07 Genomic Profiling Systems, Inc. Rapid and sensitive detection of molecules
AU2002341898A2 (en) * 2001-09-28 2003-04-07 University Of Delaware Polymorphism detection and separation
JP2005521410A (ja) 2002-03-29 2005-07-21 ジェネンテック・インコーポレーテッド 核酸分析試料の検出と定量化のための方法及び組成物
US7727720B2 (en) * 2002-05-08 2010-06-01 Ravgen, Inc. Methods for detection of genetic disorders
JP4457001B2 (ja) * 2002-05-31 2010-04-28 セクレタリー・デパートメント・オブ・アトミック・エナジー ドナー／アクセプター部分が相補鎖上となる標的核酸検出のｍｅｔ／ｆｒｅｔに基づく方法
US20040171075A1 (en) * 2002-12-31 2004-09-02 Flynn Daniel L Modulation of protein functionalities
CA2516299A1 (en) * 2003-02-18 2004-09-02 Applera Corporation Compositions and methods for multiplex analysis of polynucleotides
US20050069895A1 (en) * 2003-08-29 2005-03-31 Applera Corporation Compositions, methods, and kits for fabricating coded molecular tags
US20050064435A1 (en) 2003-09-24 2005-03-24 Xing Su Programmable molecular barcodes
US7727721B2 (en) * 2005-03-08 2010-06-01 California Institute Of Technology Hybridization chain reaction amplification for in situ imaging
WO2007001986A2 (en) 2005-06-20 2007-01-04 Yuling Luo Methods of detecting nucleic acids in individual cells and of identifying rare cells from large heterogeneous cell populations
US20090081688A1 (en) 2005-06-20 2009-03-26 Advanced Cell Diagnostics Methods of detecting nucleic acids in individual cells and of identifying rare cells from large heterogeneous cell populations
WO2007045998A2 (en) 2005-07-01 2007-04-26 Dako Denmark A/S New nucleic acid base pairs
US20080269068A1 (en) * 2007-02-06 2008-10-30 President And Fellows Of Harvard College Multiplex decoding of sequence tags in barcodes
ES2614810T3 (es) * 2008-08-14 2017-06-02 Nanostring Technologies, Inc Nanoindicadores estables
WO2010056513A2 (en) 2008-10-30 2010-05-20 Sequenom, Inc. Products and processes for multiplex nucleic acid identification
US8309306B2 (en) * 2008-11-12 2012-11-13 Nodality, Inc. Detection composition
US20100323348A1 (en) 2009-01-31 2010-12-23 The Regents Of The University Of Colorado, A Body Corporate Methods and Compositions for Using Error-Detecting and/or Error-Correcting Barcodes in Nucleic Acid Amplification Process
US20100221708A1 (en) * 2009-03-02 2010-09-02 Yamada N Alice Method for chromosome enumeration
US20100304994A1 (en) * 2009-06-02 2010-12-02 President And Fellows Of Havard College Oligonucleotide Paints
CN107267596A (zh) * 2009-06-15 2017-10-20 考利达基因组股份有限公司 用于长片段阅读测序的方法和组合物
WO2011038403A1 (en) 2009-09-28 2011-03-31 Yuling Luo Methods of detecting nucleic acid sequences with high specificity
US9677125B2 (en) † 2009-10-21 2017-06-13 General Electric Company Detection of plurality of targets in biological samples
US8965076B2 (en) * 2010-01-13 2015-02-24 Illumina, Inc. Data processing system and methods
WO2011106583A1 (en) 2010-02-26 2011-09-01 Ventana Medical Systems, Inc. Polytag probes
WO2011112634A2 (en) * 2010-03-08 2011-09-15 California Institute Of Technology Molecular indicia of cellular constituents and resolving the same by super-resolution technologies in single cells
US10266876B2 (en) * 2010-03-08 2019-04-23 California Institute Of Technology Multiplex detection of molecular species in cells by super-resolution imaging and combinatorial labeling
US10787701B2 (en) 2010-04-05 2020-09-29 Prognosys Biosciences, Inc. Spatially encoded biological assays
AU2011274369A1 (en) * 2010-07-02 2012-12-06 Ventana Medical Systems, Inc. Hapten conjugates for target detection
US8962241B2 (en) * 2010-07-20 2015-02-24 California Institute Of Technology Triggered molecular geometry based bioimaging probes
KR102085242B1 (ko) * 2011-05-17 2020-03-05 디엑스테리티 다이아그노스틱스 인코포레이티드 표적 핵산 검출을 위한 방법 및 조성물
ES2952728T3 (es) 2011-12-22 2023-11-03 Harvard College Métodos para la detección de analitos
US20140073520A1 (en) * 2011-12-23 2014-03-13 California Institute Of Technology Imaging chromosome structures by super-resolution fish with single-dye labeled oligonucleotides
US9783841B2 (en) 2012-10-04 2017-10-10 The Board Of Trustees Of The Leland Stanford Junior University Detection of target nucleic acids in a cellular sample
US20140242581A1 (en) * 2013-01-23 2014-08-28 Reproductive Genetics And Technology Solutions, Llc Compositions and methods for genetic analysis of embryos
CN110669826B (zh) * 2013-04-30 2025-01-07 加州理工学院 通过顺序杂交编条形码的分子多重标记
US20160369329A1 (en) * 2013-04-30 2016-12-22 California Institute Of Technology Multiplex labeling of molecules by sequential hybridization barcoding using probes with cleavable linkers
US20150225801A1 (en) 2014-02-11 2015-08-13 California Institute Of Technology Recording and mapping lineage information and molecular events in individual cells
US20180142307A1 (en) 2014-02-11 2018-05-24 California Institute Of Technology Recording and mapping lineage information and molecular events in individual cells
US10872679B2 (en) 2014-07-17 2020-12-22 California Institute Of Technology Multiplex analysis of molecules in single cells by image correlation
ES3014093T3 (en) 2014-07-30 2025-04-16 Harvard College Method for determining nucleic acids
US12421540B2 (en) * 2016-08-01 2025-09-23 California Institute Of Technology Sequential probing of molecular targets based on pseudo-color barcodes with embedded error correction mechanism

Also Published As

Publication number Publication date
DK2992115T3 (da) 2020-06-02
JP2020028295A (ja) 2020-02-27
US12305224B2 (en) 2025-05-20
KR20220029760A (ko) 2022-03-08
US20250043340A1 (en) 2025-02-06
US10457980B2 (en) 2019-10-29
EP2992115A2 (en) 2016-03-09
CN110669826A (zh) 2020-01-10
DK2992115T4 (da) 2025-05-19
US20200080139A1 (en) 2020-03-12
US20230295697A1 (en) 2023-09-21
US20230212658A1 (en) 2023-07-06
KR102368591B1 (ko) 2022-02-25
EP2992115A4 (en) 2016-12-14
JP2022115923A (ja) 2022-08-09
WO2014182528A2 (en) 2014-11-13
EP3626833A1 (en) 2020-03-25
KR20160003814A (ko) 2016-01-11
US11473129B2 (en) 2022-10-18
CN105392898A (zh) 2016-03-09
FI2992115T4 (fi) 2025-05-15
US20250263784A1 (en) 2025-08-21
EP2992115B1 (en) 2020-03-04
EP2992115B2 (en) 2025-03-12
WO2014182528A3 (en) 2015-01-22
JP2016518843A (ja) 2016-06-30
CN105392898B (zh) 2019-11-01
KR102701095B1 (ko) 2024-08-29
US20150267251A1 (en) 2015-09-24
JP6605452B2 (ja) 2019-11-13
CN110669826B (zh) 2025-01-07

Similar Documents

Publication Publication Date Title
US12305224B2 (en) Multiplex labeling of molecules by sequential hybridization barcoding
US20160369329A1 (en) Multiplex labeling of molecules by sequential hybridization barcoding using probes with cleavable linkers
US10510435B2 (en) Error correction of multiplex imaging analysis by sequential hybridization
CN111699268B (zh) 通过用探针的快速切换和再杂交进行顺序杂交编条形码来多重标记分子
CA2735197C (en) Imaging individual mrna molecules using multiple singly labeled probes
CA2826384C (en) A method for detecting chromosome structure and gene expression simultaneously in single cells
US20250059592A1 (en) Suppression of non-specific signals by exonucleases in fish experiment
WO2022250774A9 (en) Linked amplification tethered with exponential radiance

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424

EEER Examination request

Effective date: 20190424