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1. 发明申请

WO2016075204A1 METHODS AND ARRAYS FOR PRODUCING AND SEQUENCING MONOCLONAL CLUSTERS OF NUCLEIC ACID 审中-公开
标题翻译：用于生产和测序核酸单核苷酸的方法和阵列
公开(公告)号：WO2016075204A1
公开(公告)日：2016-05-19
申请号：PCT/EP2015/076353
申请日：2015-11-11
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LTD.
发明人： GUNDERSON, Kevin L. , BAI, Jingwei , KELLINGER, Matthew William , BEIERLE, John M. , BOUTELL, Jonathan Mark , RIGATTI, Roberto , ROGERT BACIGALUPO, Maria Candelaria , BOYANOV, Boyan , MAISINGER, Klaus
IPC分类号： C12Q1/68 , B01J19/00 , C40B40/06 , C40B50/14
CPC分类号： C12Q1/6874 , B01J19/0046 , B01J2219/00317 , B01J2219/00585 , B01J2219/00596 , B01J2219/00608 , B01J2219/00637 , B01J2219/00722 , C12Q1/6806 , C12Q1/6837 , C12Q1/6853 , C40B40/06 , C40B50/14 , C12Q2565/513 , C12Q2565/543
摘要： Methods for capturing and amplifying target polynucleotides on a solid surface, in particular in a well in a microarray, wherein the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; b) a first layer covering the inner well surface and comprising at least one first capture primer pair; and c) a second layer covering the first layer and the surface surrounding the well. Alternatively, the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; and b) a layer covering the inner well surface and comprising at least one first capture primer pair and at least one second capture primer pair. In particular kinetic exclusion amplification is used in creating monoclonal populations of the nucleic acids in the wells. The application also discloses a method for modifying an immobilized capture primer comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of template nucleic acids to produce one or more immobilized template nucleic acids,wherein the plurality of immobilized capture primers comprises a first plurality of primers comprising a 3'-terminal universal capture region Y, e.g. primer P5, and a second plurality of primers comprising a 3'-terminal universal capture region Z, e.g. primer P7; and wherein each template nucleic acid is flanked by a 5'-terminal and a 3'-terminal universal capture region Y or Z and comprises one or more, e.g. SapI, restriction sites and a target-specific capture region between the one or more restriction sites and the 3'-terminal universal capture region; and b) extending one or more immobilized capture primer. Finally, the application discloses a method for modifying an immobilized capture primer comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of different seed nucleic acids to produce a plurality of different immobilized seed nucleic acids; b) extending two or more of the immobilized capture primers to produce a plurality of different immobilized extension products complementary to two or more of the plurality of different immobilized seed nucleic acids; and c) activating one immobilized extension product of the plurality of different immobilized extension products, to form an activated capture primer.
摘要翻译：用于在固体表面上特别是在微阵列中的阱中捕获和扩增靶多核苷酸的方法，其中所述微阵列可以包括a）包含至少一个阱的衬底，围绕所述阱的表面和内部阱表面; b）覆盖所述内部孔表面并包含至少一个第一捕获引物对的第一层; 以及c）覆盖所述第一层和围绕所述孔的表面的第二层。或者，微阵列可以包括：a）包含至少一个阱的衬底，围绕阱的表面和内部阱表面; 以及b）覆盖所述内部孔表面并包含至少一个第一捕获引物对和至少一个第二捕获引物对的层。特别地，动力学排除扩增用于产生孔中核酸的单克隆群体。本申请还公开了一种修饰固定化捕获引物的方法，其包括：a）使包含多个固定的捕获引物的底物与多个模板核酸接触以产生一种或多种固定的模板核酸，其中所述多个固定的捕获引物包括包含3'末端通用捕获区Y的第一多个引物，例如引物P5和包含3'末端通用捕获区Z的第二多个引物。引物P7; 并且其中每个模板核酸侧接有5'-末端和3'末端通用捕获区Y或Z，并且包含一个或多个，例如， SapI，限制性位点和一个或多个限制性位点与3'-末端通用捕获区之间的靶标特异性捕获区域; 和b）延伸一个或多个固定的捕获引物。最后，本申请公开了一种用于修饰固定化捕获引物的方法，其包括：a）使包含多个固定的捕获引物的底物与多种不同的种子核酸接触以产生多种不同的固定化种子核酸; b）延伸两个或更多个固定的捕获引物以产生与所述多个不同固定化种子核酸中的两种或更多种互补的多种不同的固定化延伸产物; 和c）激活所述多个不同的固定化延伸产物的一个固定化的延伸产物，以形成活化的捕获引物。

2. 发明申请

WO2012106081A2 METHODS FOR REDUCING NUCLEIC ACID DAMAGE 审中-公开
标题翻译：降低核酸损伤的方法
公开(公告)号：WO2012106081A2
公开(公告)日：2012-08-09
申请号：PCT/US2012/021040
申请日：2012-01-12
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LTD. , KLAUSING, Kay , SHEN, Min-Jui Richard , MOORE, John , SMITH, Vincent , HALL, Kevin , GORMLEY, Niall Anthony , IOANNOU, Avgousta , FRITZILAS, Epameinondas , RIGATTI, Roberto
发明人： KLAUSING, Kay , SHEN, Min-Jui Richard , MOORE, John , SMITH, Vincent , HALL, Kevin , GORMLEY, Niall Anthony , IOANNOU, Avgousta , FRITZILAS, Epameinondas , RIGATTI, Roberto
IPC分类号： C12Q1/68 , C12Q1/48 , G01N33/53
CPC分类号： C12P19/34 , C12N15/1003 , C12Q1/6806 , C12Q2521/531 , C12Q2527/125 , C12Q2563/131
摘要： Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample.
摘要翻译：本文提供了一种在选择片段化和检测的核酸加工步骤期间抑制核酸降解的方法，包括在加工步骤期间使核酸与包含没食子酸，其类似物，衍生物或其混合物的溶液接触，其中所述接触抑制核酸的降解。本文还提供抑制光诱导的核酸降解的方法。此外，本文提供的是在制备核酸样品期间减少或抑制核酸损伤的方法，包括在包含一种或多种化合物的溶液中碎片样品中的核酸序列，所述化合物抑制核酸序列的降解样品。

3. 发明申请

WO2012025250A1 METHODS FOR PAIRED - END SEQUENCING OF POLYNUCLEOTIDES 审中-公开
标题翻译：多核苷酸配对方法
公开(公告)号：WO2012025250A1
公开(公告)日：2012-03-01
申请号：PCT/EP2011/004328
申请日：2011-08-29
申请人： ILLUMINA CAMBRIDGE LTD. , RIGATTI, Roberto , GORMLEY, Niall, A. , BOUTELL, Jonathan, Mark
发明人： RIGATTI, Roberto , GORMLEY, Niall, A. , BOUTELL, Jonathan, Mark
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q2535/119 , C12Q2535/122 , C12Q2565/513 , C12Q2565/543
摘要： Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.
摘要翻译：本文提供了用于测序多核苷酸分子的方法。该方法包括提供连接到表面的多个多核苷酸分子的步骤，其中每个多核苷酸分子的第一部分连接到该表面的第一位置，并且每个多核苷酸分子的第二部分连接到该多核苷酸分子的第二位置表面，第一和第二位置的相对接近度与第一和第二部分配对的概率相关，分离表面上的多核苷酸分子的第一和第二部分，确定第一和第二部分的序列多核苷酸分子，并比较相对接近度和序列以确定哪个第一和第二部分配对并确定靶多核苷酸分子的序列。

4. 发明申请

WO2010003132A1 USING POPULATIONS OF BEADS FOR THE FABRICATION OF ARRAYS ON SURFACES 审中-公开
标题翻译：使用人造丝来制作表面阵列
公开(公告)号：WO2010003132A1
公开(公告)日：2010-01-07
申请号：PCT/US2009/049636
申请日：2009-07-02
申请人： ILLUMINA CAMBRIDGE LTD. , RIGATTI, Roberto , SMITH, Geoffrey, Paul , BOUTELL, Jonathan, Mark , ROSENMAN, Stephen, J.
发明人： RIGATTI, Roberto , SMITH, Geoffrey, Paul , BOUTELL, Jonathan, Mark
IPC分类号： C12P19/34
CPC分类号： C12N15/1068 , B01J19/0046 , C12Q1/6837 , C12Q1/6874 , C12Q2565/543 , C12Q2565/537 , C12Q2563/149 , C12Q2563/161
摘要： The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.
摘要翻译：本发明提供了基于从多个珠粒转移到表面的内容来在表面上创建特征阵列的方法。可以使用包括以下步骤的方法转移核酸含量：（a）提供具有附着于所述表面的一种或多种引物寡核苷酸的表面; （b）提供珠池，其中所述池中的珠子具有连接到其上的多个模板，所述多个模板包含单个核酸模板序列的多个拷贝; （c）通过将模板与引物寡核苷酸杂交将珠子排列在表面上; 和（d）扩展引物以产生附着在表面上的模板的拷贝。

5. 发明申请

WO2016130704A2 METHODS AND COMPOSITIONS FOR ANALYZING CELLULAR COMPONENTS 审中-公开
标题翻译：分析细胞成分的方法和组合物
公开(公告)号：WO2016130704A2
公开(公告)日：2016-08-18
申请号：PCT/US2016/017391
申请日：2016-02-10
申请人： ILLUMINA, INC.
发明人： GUNDERSON, Kevin L. , STEEMERS, Frank J. , FISHER, Jeffrey S. , RIGATTI, Roberto
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q2537/143 , C12Q2563/149 , C12Q2563/159 , C12Q2563/185
摘要： Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.
摘要翻译：本发明的实施例涉及分析小区的组件。在一些实施例中，本发明涉及分析单个小区的组件。在一些实施方案中，所述方法和组合物涉及测序核酸。在一些实施方案中，所述方法和组合物涉及鉴定和/或定量核酸，蛋白质，细胞器和/或细胞代谢物。

6. 发明申请

WO2012050920A1 COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS 审中-公开
标题翻译：用于测序核酸的组合物和方法
公开(公告)号：WO2012050920A1
公开(公告)日：2012-04-19
申请号：PCT/US2011/053763
申请日：2011-09-28
申请人： ILLUMINA, INC. , BOUTELL, Jonathan, Mark , RIGATTI, Roberto , BETLEY, Jason, Richard , GORMLEY, Niall, Anthony
发明人： BOUTELL, Jonathan, Mark , RIGATTI, Roberto , BETLEY, Jason, Richard , GORMLEY, Niall, Anthony
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q2525/101 , C12Q2525/186 , C12Q2525/191 , C12Q2565/543 , C12Q2565/537 , C12Q2535/122 , C12Q2523/301 , C12Q2521/319
摘要： Disclosed herein are compositions and methods for sequencing nucleic acids.
摘要翻译：本文公开了用于测序核酸的组合物和方法。

7. 发明申请

WO2011106368A2 AMPLIFICATION METHODS TO MINIMISE SEQUENCE SPECIFIC BIAS 审中-公开
标题翻译：最小化序列特异性偏差的放大方法
公开(公告)号：WO2011106368A2
公开(公告)日：2011-09-01
申请号：PCT/US2011/025851
申请日：2011-02-23
申请人： ILLUMINA, INC. , RIGATTI, Roberto , BOUTELL, Jonathan Mark , SHEN, Min-Jui Richard
发明人： RIGATTI, Roberto , BOUTELL, Jonathan Mark , SHEN, Min-Jui Richard
IPC分类号： C12Q1/68 , C12N15/10
CPC分类号： C12P19/34 , C09K3/00 , C12Q1/686 , C12Q2565/518 , C12Q2527/137
摘要： Methods for amplifying nucleic acids are provided. The methods can be used to minimise sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimising GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilising flow cells
摘要翻译：提供了扩增核酸的方法。这些方法可以用于最小化由某些核酸序列的优先扩增引起的序列特异性偏差。描述了可以降低AT富含模板相对于GC富集模板的效率的方法，由此使具有不同序列的多个模板的扩增反应期间的GC偏差最小化。该方法适用于固相扩增，例如利用流动池

8. 发明申请

WO2012055929A1 SEQUENCING METHODS 审中-公开
标题翻译：序列方法
公开(公告)号：WO2012055929A1
公开(公告)日：2012-05-03
申请号：PCT/EP2011/068790
申请日：2011-10-26
申请人： ILLUMINA, INC. , RIGATTI, Roberto , BOUTELL, Jonathan, Mark , BETLEY, Jason, Richard , GORMLEY, Niall, Anthony , RONAGHI, Mostafa , EVERS, Dirk
发明人： RIGATTI, Roberto , BOUTELL, Jonathan, Mark , BETLEY, Jason, Richard , GORMLEY, Niall, Anthony , RONAGHI, Mostafa , EVERS, Dirk
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q2565/514 , C12Q2537/155 , C12Q2525/186 , C12Q2525/185 , C12Q2537/113 , C12Q2525/204
摘要： The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.
摘要翻译：本技术涉及分子科学，如基因组学。更具体地，本技术涉及核酸测序。

9. 发明申请

WO2011025477A1 METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES 审中-公开
标题翻译：选择和放大多核苷酸的方法
公开(公告)号：WO2011025477A1
公开(公告)日：2011-03-03
申请号：PCT/US2009/054945
申请日：2009-08-25
申请人： ILLUMINA, INC. , SABOT, Andrea , RIGATTI, Roberto , SHEN, Min-jui, Richard
发明人： SABOT, Andrea , RIGATTI, Roberto , SHEN, Min-jui, Richard
IPC分类号： C12P19/34
CPC分类号： C12N15/1068 , C12Q1/6806 , C12Q1/6837 , C12Q1/6874 , C12Q2565/543 , C12Q2565/507 , C12Q2531/107
摘要： The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.
摘要翻译：本发明提供了控制固体支持物表面上不同分子种类的密度的方法。将不同分子种类的第一混合物连接到固体支持物上，以便以期望的密度附着每种物质，从而产生具有附着捕获分子的衍生化载体。衍生的载体用不同分子种类的第二混合物处理，其中第二混合物中的不同分子物质特异性地结合到固相载体上的不同捕获分子。一个或多个捕获分子可以被可逆地修饰，使得捕获分子在分子物质的第二混合物附着之前和之后具有不同的活性。在具体实施方案中，不同的分子种类是可逆修饰以在扩增反应中具有不同活性的核酸。

10. 发明公开

EP3725893A1 COMPOSITIONS FOR ANALYZING CELLULAR COMPONENTS 审中-公开
公开(公告)号：EP3725893A1
公开(公告)日：2020-10-21
申请号：EP20165203.9
申请日：2016-02-10
申请人： Illumina, Inc.
发明人： FISHER, Jeffrey S. , GUNDERSON, Kevin L. , RIGATTI, Roberto , STEEMERS, Frank J.
IPC分类号： C12Q1/6806
摘要： Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.

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