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61. 发明申请

US20160251700A1 NUCLEIC ACID SAMPLE PREPARATION 有权
标题翻译：核酸样品制备
公开(公告)号：US20160251700A1
公开(公告)日：2016-09-01
申请号：US15054227
申请日：2016-02-26
申请人： Tobias William Barr OST , Neil Matthew BELL
发明人： Tobias William Barr OST , Neil Matthew BELL
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q1/6855 , C12Q1/6869 , C12Q1/6874 , C12Q2521/131 , C12Q2523/107 , C12Q2523/125 , C12Q2525/121 , C12Q2525/301 , C12Q2535/122 , C12Q2525/186 , C12Q2525/191 , C12Q2543/101 , C12Q2565/1015
摘要： This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.
摘要翻译：本发明涉及用于分析的核酸样品的制备。本发明对于单链样品可能特别有用。本发明的实施方案涉及在制备核酸测序文库中使用模板无关聚合酶连接双链或发夹寡核苷酸。

62. 发明申请

US20150344942A1 METHODS AND PRODUCT FOR OPTIMISING LOCALISED OR SPATIAL DETECTION OF GENE EXPRESSION IN A TISSUE SAMPLE 有权
标题翻译：用于优化组织样品中基因表达的局部或空间检测的方法和产品
公开(公告)号：US20150344942A1
公开(公告)日：2015-12-03
申请号：US14434274
申请日：2013-10-16
申请人： SPATIAL TRANSCRIPTOMICS AB
发明人： JONAS FRISEN , PATRIK STAHL , JOAKIM LUNDEBERG , FREDRIK SALMEN
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q1/6841 , C12Q1/6874 , C12Q2543/101 , C12Q2565/514 , C12Q2565/537
摘要： The present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3′ end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridise to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c).
摘要翻译：本发明涉及用于组织样本或其部分中RNA的局部或空间检测和/或分析的方法和产品，其包括：（a）提供对象底物，其上至少一种捕获探针，其包含捕获结构域直接或间接固定，使得探针定向为具有游离的3'末端以使所述探针用作逆转录酶（RT）引物; （b）使所述底物与组织样品接触并允许组织样品的RNA与捕获探针杂交; （c）使用所述捕获探针作为RT引物从捕获的RNA分子产生cDNA分子; （d）标记步骤（c）中产生的cDNA分子，其中所述标记步骤可以与所述生成步骤同时或之后; （e）检测来自标记的cDNA分子的信号; 以及任选地（f）对所述组织样品进行成像，其中所述组织样品在步骤（c）之前或之后成像。

63. 发明申请

US20140302496A1 MULTIMODAL METHODS FOR SIMULTANEOUS DETECTION AND QUANTIFICATION OF MULTIPLE NUCLEIC ACIDS IN A SAMPLE 有权
标题翻译：用于样品中多种核酸的同时检测和定量的多模式方法
公开(公告)号：US20140302496A1
公开(公告)日：2014-10-09
申请号：US14153550
申请日：2014-01-13
申请人： PRIMERADX, INC.
发明人： Jork Nolling , Vincent Miles
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6813 , C12Q1/6844 , C12Q1/686 , C12Q2521/107 , C12Q2525/191 , C12Q2537/143 , C12Q2543/101
摘要： Described herein are approaches for the detection, identification, and/or quantification of target nucleic acids, including, but not limited to partially, substantially randomly, degraded target nucleic acids, in a biological sample, such as a formalin-fixed, paraffin-embedded (FFPE) sample. These approaches provide a means of detecting, identifying, and/or quantifying target nucleic acid molecules, including DNA and RNA molecules, further including RNAs of different classes, from the same sample, and in the same reaction, by using “expander oligonucleotides,” as the term is defined herein, to convert fragments of target nucleic acids into discretely sized DNA fragments, each with a chosen length characteristic for the target nucleic acid from which it is derived.
摘要翻译：本文描述了用于检测，鉴定和/或定量目标核酸的方法，所述靶核酸包括但不限于生物样品中的部分基本随机降解的靶核酸，例如福尔马林固定的，石蜡包埋的（FFPE）样品。这些方法提供了检测，鉴定和/或定量靶核酸分子（包括DNA和RNA分子）的手段，其进一步包括来自相同样品的不同类别的RNA，并且在相同的反应中，通过使用“扩增寡核苷酸” 如本文所定义的，将靶核酸的片段转化成离散尺寸的DNA片段，每个DNA片段具有从其衍生的靶核酸的所选长度特征。

64. 发明申请

US20140256575A1 SYNTHESIS OF LONG FISH PROBES 有权
标题翻译：合成长鱼探针
公开(公告)号：US20140256575A1
公开(公告)日：2014-09-11
申请号：US14146216
申请日：2014-01-02
申请人： Agilent Technologies, Inc.
发明人： Emily Marine Leproust , Siyuan Chen , Michael Ruvolo
IPC分类号： C12Q1/68 , G06F19/20
CPC分类号： C12Q1/6841 , C12Q1/6883 , C12Q1/6886 , G06F19/20 , C12Q2531/113 , C12Q2533/107 , C12Q2543/101
摘要： A method comprising: synthesizing a set of overlapping oligonucleotides that comprises probe sequences that hybridize to unique sequences in a chromosome, assembling the overlapping oligonucleotides in a way that produces one or more double stranded polynucleotides that each comprises multiple probe sequences, labeling the one or more double stranded polynucleotides to produce one or more labeled probes, and hybridizing the labeled probes to an intact chromosome, in situ, is provided.
摘要翻译：一种方法，包括：合成一组重叠的寡核苷酸，其包含与染色体中的唯一序列杂交的探针序列，以产生一个或多个双链多核苷酸的方式组装重叠的寡核苷酸，每个双链多核苷酸各自包含多个探针序列，标记所述一个或多个提供双链多核苷酸以产生一个或多个标记的探针，并将标记的探针与原位染色体杂交。

65. 发明申请

US20090258351A1 Methods and Reagents for Combined PCR Amplification 失效
标题翻译：组合PCR扩增的方法和试剂
公开(公告)号：US20090258351A1
公开(公告)日：2009-10-15
申请号：US12193667
申请日：2008-08-18
申请人： Paul E. Mayrand
发明人： Paul E. Mayrand
IPC分类号： C12Q1/68 , C07H21/04 , C12P19/34
CPC分类号： C12Q1/6818 , C07H21/04 , C12Q1/6853 , C12Q1/686 , Y10S435/81 , Y10S435/911 , C12Q2565/107 , C12Q2565/1015 , C12Q2525/186 , C12Q2525/125 , C12Q2543/101 , C12Q2537/101 , C12Q2563/113 , C12Q2531/113 , C12Q2527/101 , C12Q2521/513
摘要： An oligonucleotide probe is disclosed, the probe including an oligonucleotide, a fluorescer molecule attached to a first end of the oligonucleotide and a quencher molecule attached to the opposite end of the oligonucleotide. The probe is rendered impervious to digestion by the 5′→3′ exonuclease activity of a polymerase and the 5′→3′ extension of by a polymerase. The invention also includes methods for performing combined PCR amplification and hybridization probing, one such method including the steps of contacting a target nucleic acid sequence with PCR reagents and an oligonucleotide probe as described above, and subjecting these reagents to thermal cycling. One preferred refinement of the above method further includes the addition of a strand displacer to facilitate amplification. Additional similar combined PCR hybridization methods are disclosed, such methods not requiring probes having their 5′ ends protected, wherein (i) the polymerase lacks 5′→3′ exonuclease activity, (ii) a 5′→3′ exonuclease inhibitor is included, and (iii) an exonuclease deactivation step is performed.
摘要翻译：公开了寡核苷酸探针，所述探针包含寡核苷酸，附着于寡核苷酸第一末端的荧光分子和连接于寡核苷酸相对末端的猝灭剂分子。该探针不被聚合酶的5'→3'核酸外切酶活性消化，并且通过聚合酶的5'→3'延伸。本发明还包括用于进行组合PCR扩增和杂交探测的方法，一种这样的方法包括如下步骤：使靶核酸序列与PCR试剂和如上所述的寡核苷酸探针接触，并对这些试剂进行热循环。上述方法的一个优选的改进还包括添加链置换剂以促进扩增。公开了另外类似的组合PCR杂交方法，这种方法不需要其5'末端被保护的探针，其中（i）聚合酶缺乏5'→3'核酸外切酶活性，（ii）5'→3'外切核酸酶抑制剂包括，和（iii）进行外切核酸酶失活步骤。

66. 发明授权

US07413708B2 Methods and reagents for combined PCR amplification 失效
标题翻译：组合PCR扩增的方法和试剂
公开(公告)号：US07413708B2
公开(公告)日：2008-08-19
申请号：US11775151
申请日：2007-07-09
申请人： Paul E. Mayrand
发明人： Paul E. Mayrand
IPC分类号： B01L3/00 , C07H21/04 , C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6818 , C07H21/04 , C12Q1/6853 , C12Q1/686 , Y10S435/81 , Y10S435/911 , C12Q2565/107 , C12Q2565/1015 , C12Q2525/186 , C12Q2525/125 , C12Q2543/101 , C12Q2537/101 , C12Q2563/113 , C12Q2531/113 , C12Q2527/101 , C12Q2521/513
摘要： An oligonucleotide probe is disclosed, the probe including an oligonucleotide, a fluorescer molecule attached to a first end of the oligonucleotide and a quencher molecule attached to the opposite end of the oligonucleotide. The probe is rendered impervious to digestion by the 5′→3′ exonuclease activity of a polymerase and the 5′→3′ extension of by a polymerase. The invention also includes methods for performing combined PCR amplification and hybridization probing, one such method including the steps of contacting a target nucleic acid sequence with PCR reagents and an oligonucleotide probe as described above, and subjecting these reagents to thermal cycling. One preferred refinement of the above method further includes the addition of a strand displacer to facilitate amplification. Additional similar combined PCR hybridization methods are disclosed, such methods not requiring probes having their 5′ ends protected, wherein (i) the polymerase lacks 5′→3′ exonuclease activity, (ii) a 5′→3′ exonuclease inhibitor is included, and (iii) an exonuclease deactivation step is performed.
摘要翻译：公开了寡核苷酸探针，所述探针包含寡核苷酸，附着于寡核苷酸第一末端的荧光分子和连接于寡核苷酸相对末端的猝灭剂分子。该探针不被聚合酶的5'→3'核酸外切酶活性消化，并且通过聚合酶的5'→3'延伸。本发明还包括用于进行组合PCR扩增和杂交探测的方法，一种这样的方法包括如下步骤：使靶核酸序列与PCR试剂和如上所述的寡核苷酸探针接触，并对这些试剂进行热循环。上述方法的一个优选的改进还包括添加链置换剂以促进扩增。公开了另外类似的组合PCR杂交方法，这种方法不需要其5'末端被保护的探针，其中（i）聚合酶缺少5'→3'核酸外切酶活性，（ii）5'→3'外切核酸酶抑制剂包括，和（iii）进行外切核酸酶失活步骤。

67. 发明申请

US20050227247A1 Methods and reagents for combined PCR amplification and hybridization probing 失效
标题翻译：用于组合PCR扩增和杂交探测的方法和试剂
公开(公告)号：US20050227247A1
公开(公告)日：2005-10-13
申请号：US10946458
申请日：2004-09-20
申请人： Paul Maynard
发明人： Paul Maynard
IPC分类号： C12N15/09 , C07H21/04 , C12P19/34 , C12Q1/68 , G01N21/64 , G01N21/77 , G01N21/78 , G01N33/53 , G01N33/566
CPC分类号： C12Q1/6818 , C07H21/04 , C12Q1/6853 , C12Q1/686 , Y10S435/81 , Y10S435/911 , C12Q2565/107 , C12Q2565/1015 , C12Q2525/186 , C12Q2525/125 , C12Q2543/101 , C12Q2537/101 , C12Q2563/113 , C12Q2531/113 , C12Q2527/101 , C12Q2521/513
摘要： An oligonucleotide probe is disclosed, the probe including an oligonucleotide, a fluorescer molecule attached to a first end of the oligonucleotide and a quencher molecule attached to the opposite end of the oligonucleotide. The probe is rendered impervious to digestion by the 5′→3′ exonuclease activity of a polymerase and the 5′→3′ extension of by a polymerase. The invention also includes methods for performing combined PCR amplification and hybridization probing, one such method including the steps of contacting a target nucleic acid sequence with PCR reagents and an oligonucleotide probe as described above, and subjecting these reagents to thermal cycling. One preferred refinement of the above method further includes the addition of a strand displacer to facilitate amplification. Additional similar combined PCR hybridization methods are disclosed, such methods not requiring probes having their 5′ ends protected, wherein (i) the polymerase lacks 5′→3′ exonuclease activity, (ii) a 5′→3′ exonuclease inhibitor is included, and (iii) an exonuclease deactivation step is performed.
摘要翻译：公开了寡核苷酸探针，所述探针包含寡核苷酸，附着于寡核苷酸第一末端的荧光分子和连接于寡核苷酸相对末端的猝灭剂分子。该探针不被聚合酶的5'→3'核酸外切酶活性消化，并且通过聚合酶的5'→3'延伸。本发明还包括用于进行组合PCR扩增和杂交探测的方法，一种这样的方法包括如下步骤：使靶核酸序列与PCR试剂和如上所述的寡核苷酸探针接触，并使这些试剂进行热循环。上述方法的一个优选的改进还包括添加链置换剂以促进扩增。公开了另外类似的组合PCR杂交方法，这种方法不需要其5'末端被保护的探针，其中（i）聚合酶缺乏5'→3'核酸外切酶活性，（ii）5'→3'核酸外切酶抑制剂包括，和（iii）进行外切核酸酶失活步骤。

68. 发明授权

US06703247B1 Apparatus and methods for efficient processing of biological samples on slides 失效
标题翻译：用于在载玻片上有效处理生物样品的装置和方法
公开(公告)号：US06703247B1
公开(公告)日：2004-03-09
申请号：US09219443
申请日：1998-12-23
申请人： Wei-Sing Chu
发明人： Wei-Sing Chu
IPC分类号： G01N110
CPC分类号： C12Q1/6841 , B01L7/52 , C12Q1/686 , G01N1/312 , Y10T436/112499 , Y10T436/2575 , C12Q2543/101
摘要： Slideholders which are useful for manually or automatically processing biological samples on microscope slides are described. These slideholders hold multiple slides and are designed in conjunction with specialized trays for rapidly processing the mounted biological samples such as for immunocytochemical staining. The slideholder plus tray assemblies incorporate several useful advantages including a requirement for minimal reaction fluid volumes, ease of handling several slides concurrently, prevention of evaporation of reaction fluids, protection of the biological sample from extraneous environmental contamination, and the ability to perform in situ PCR. Various aspects of the design aid in removing trapped air from the reaction fluids and in adding fluids to the biological sample. One embodiment comprises a coverstip with a soft top which aids in prevention of tissue degradation by preventing pressure buildup during PCR. The system results in very low background signals and allows for manually processing manifold times the number of slides as is typically possible with other current manual methods. Another aspect of the invention is the use of predried reagents in wells, especially the use of predried reagents which dissolve sequentially. Yet another aspect of the invention is the use of external controls placed directly on a microscope slide in conjunction with a biological sample to be assayed. The external controls can be conveniently placed on a membrane which can be affixed to the slide. A further aspect of the invention is a specially designed tray to allow whole chromosome painting of all chromosomes of a cell sample on a single slide.
摘要翻译：描述了用于在显微镜载玻片上手动或自动处理生物样品的载玻片。这些滑块具有多个载玻片，并与专门的托盘一起设计，用于快速处理安装的生物样品，如免疫细胞化学染色。载玻片加托盘组件包含几个有用的优点，包括对反应液体体积最小的要求，容易同时处理几个载玻片，防止反应流体蒸发，保护生物样品免受外部环境污染，以及执行原位PCR的能力。该设计的各个方面有助于从反应流体中除去捕获的空气并向生物样品中添加流体。一个实施方案包括具有柔软顶部的覆盖片，其有助于通过防止PCR期间的压力累积来防止组织降解。该系统产生非常低的背景信号，并且允许手动处理幻灯片的数量，这与其他当前的手动方法通常是可能的。本发明的另一方面是在孔中使用预干燥的试剂，特别是使用依次溶解的预干燥试剂。本发明的另一方面是使用直接放置在显微镜载玻片上的外部对照以及要测定的生物样品。外部控制器可以方便地放置在可以固定在载玻片上的膜上。本发明的另一方面是特殊设计的托盘，以允许在单个载玻片上对细胞样品的所有染色体进行全染色体染色。

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