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    Optimization of gene expression analysis using immobilized capture probes
    1.
    发明授权
    Optimization of gene expression analysis using immobilized capture probes 有权
    使用固定化捕获探针优化基因表达分析

    公开(公告)号：US08795960B2

    公开(公告)日：2014-08-05

    申请号：US12480215

    申请日：2009-06-08

    申请人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    发明人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C12M1/34 ,  C12M3/00 ,  C07H21/04

    CPC分类号： C12Q1/6832 ,  B01J2219/00459 ,  B01J2219/00576 ,  B01J2219/00608 ,  B01J2219/00648 ,  B01J2219/00722 ,  C12Q1/6809 ,  C12Q1/6834 ,  C12Q1/6837 ,  C12Q2537/143 ,  C12Q2565/501 ,  C12Q2565/507 ,  C12Q2533/101 ,  C12Q2565/514 ,  C12Q2565/519

    摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.

    摘要翻译： 公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括 目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译 位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

    Optimization of Gene Expression Analysis using Immobilized Capture Probes
    3.
    发明申请
    Optimization of Gene Expression Analysis using Immobilized Capture Probes 有权
    使用固定化捕获探针优化基因表达分析

    公开(公告)号：US20090263820A1

    公开(公告)日：2009-10-22

    申请号：US12480215

    申请日：2009-06-08

    申请人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    发明人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6832 ,  B01J2219/00459 ,  B01J2219/00576 ,  B01J2219/00608 ,  B01J2219/00648 ,  B01J2219/00722 ,  C12Q1/6809 ,  C12Q1/6834 ,  C12Q1/6837 ,  C12Q2537/143 ,  C12Q2565/501 ,  C12Q2565/507 ,  C12Q2533/101 ,  C12Q2565/514 ,  C12Q2565/519

    摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.

    摘要翻译： 公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括 目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译 位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

    Optimization of gene expression analysis using immobilized capture probes
    4.
    发明授权
    Optimization of gene expression analysis using immobilized capture probes 有权
    使用固定化捕获探针优化基因表达分析

    公开(公告)号：US07563569B2

    公开(公告)日：2009-07-21

    申请号：US10974036

    申请日：2004-10-26

    申请人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    发明人： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C12M1/00 ,  C12M1/34 ,  C12M3/00 ,  C07H21/02 ,  C07H21/04

    CPC分类号： C12Q1/6832 ,  B01J2219/00459 ,  B01J2219/00576 ,  B01J2219/00608 ,  B01J2219/00648 ,  B01J2219/00722 ,  C12Q1/6809 ,  C12Q1/6834 ,  C12Q1/6837 ,  C12Q2537/143 ,  C12Q2565/501 ,  C12Q2565/507 ,  C12Q2533/101 ,  C12Q2565/514 ,  C12Q2565/519

    摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.

    摘要翻译： 公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括 目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译 位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

    Probe density self-considerations and elongation of complementary looped probes where probes are attached to a solid phase
    8.
    发明授权
    Probe density self-considerations and elongation of complementary looped probes where probes are attached to a solid phase 有权
    探针密度自我考虑和互补环状探针的伸长，其中探针连接到固相

    公开(公告)号：US08795966B2

    公开(公告)日：2014-08-05

    申请号：US12708362

    申请日：2010-02-18

    申请人： Michael Seul ,  Yi Zhang ,  Sukanta Banerjee ,  Jiacheng Yang ,  Chiu Chau

    发明人： Michael Seul ,  Yi Zhang ,  Sukanta Banerjee ,  Jiacheng Yang ,  Chiu Chau

    IPC分类号： C12Q1/68 ,  C07H21/04

    CPC分类号： C12Q1/6837 ,  C12Q1/6818 ,  C12Q1/6827 ,  C12Q2565/1015 ,  C12Q2537/143 ,  C12Q2533/101 ,  C12Q2535/125 ,  C12Q2525/301

    摘要： In a multiplexed assay method carried out in solution, wherein the solution contains nucleic acid targets and, wherein several different types of oligonucleotide probes, each type having a different sequence in a region designated as a target binding domain, are used to detect the nucleic acid targets, said assay method including a method for increasing the effective concentration of the nucleic acid targets at the surface of a bead to which the oligonucleotide probes are bound, by one or more of the following steps:adjusting assay conditions so as to increase the effective concentration of the targets available for binding to the probes, by one or more of the following: (i) selecting a particular probe density on the surface of the bead; (ii) selecting a solution having an ionic strength greater than a threshold; (ii) selecting a target domain of a size less than a threshold; or (iii) selecting target domains within a specified proximity to a terminal end of the targets.

    摘要翻译： 在溶液中进行的多重测定方法中，其中溶液含有核酸靶，并且其中使用几个不同类型的寡核苷酸探针，每个类型在被称为靶结合结构域的区域中具有不同序列，以检测核酸 目标，所述测定方法包括通过一个或多个以下步骤增加寡核苷酸探针结合珠粒表面上的核酸靶的有效浓度的方法：调节测定条件以增加有效 通过一种或多种以下方法可用于结合探针的靶的浓度：（i）在珠的表面上选择特定的探针密度; （ii）选择具有大于阈值的离子强度的溶液; （ii）选择小于阈值的大小的目标域; 或（iii）在目标的终端的指定接近范围内选择目标域。

    Probe density considerations and elongation of self-complementary looped probes where probes are attached to a solid phase
    9.
    发明申请
    Probe density considerations and elongation of self-complementary looped probes where probes are attached to a solid phase 审中-公开
    探头密度考虑和探针附着在固相上的自互补环状探针的伸长率

    公开(公告)号：US20070243534A1

    公开(公告)日：2007-10-18

    申请号：US11403100

    申请日：2006-04-12

    申请人： Michael Seul ,  Yi Zhang ,  Sukanta Banerjee ,  Jiacheng Yang ,  Chiu Chau

    发明人： Michael Seul ,  Yi Zhang ,  Sukanta Banerjee ,  Jiacheng Yang ,  Chiu Chau

    IPC分类号： C12Q1/68 ,  C12M3/00

    CPC分类号： C12Q1/6837 ,  C12Q1/6818 ,  C12Q1/6827 ,  C12Q2565/1015 ,  C12Q2537/143 ,  C12Q2533/101 ,  C12Q2535/125 ,  C12Q2525/301

    摘要： In a multiplexed assay method carried out in solution, wherein the solution contains nucleic acid targets and, wherein several different types of oligonucleotide probes, each type having a different sequence in a region designated as a target binding domain, are used to detect the nucleic acid targets, said assay method including a method for increasing the effective concentration of the nucleic acid targets at the surface of a bead to which the oligonucleotide probes are bound, by one or more of the following steps: adjusting assay conditions so as to increase the effective concentration of the targets available for binding to the probes, by one or more of the following: (i) selecting a particular probe density on the surface of the bead; (ii) selecting a solution having an ionic strength greater than a threshold; (ii) selecting a target domain of a size less than a threshold; or (iii) selecting target domains within a specified proximity to a terminal end of the targets.

    摘要翻译： 在溶液中进行的多重测定方法中，其中溶液含有核酸靶，并且其中使用几个不同类型的寡核苷酸探针，每个类型在被称为靶结合结构域的区域中具有不同序列，以检测核酸 目标，所述测定方法包括通过一个或多个以下步骤增加寡核苷酸探针结合珠粒表面上的核酸靶的有效浓度的方法：调节测定条件以增加有效 通过一种或多种以下方法可用于结合探针的靶的浓度：（i）在珠的表面上选择特定的探针密度; （ii）选择具有大于阈值的离子强度的溶液; （ii）选择小于阈值的大小的目标域; 或（iii）在目标的终端的指定接近范围内选择目标域。