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1. 发明申请

US20050273268A1 Method and system for quantifying and removing spatial-intensity trends in microarray data 有权
标题翻译：用于量化和消除微阵列数据中的空间强度趋势的方法和系统
公开(公告)号：US20050273268A1
公开(公告)日：2005-12-08
申请号：US10859868
申请日：2004-06-02
申请人： Jayati Ghosh , Bill Peck , Eric Leproust , Charles Troup , Glenda Delenstarr , Patrick Collins , John Corson , Paul Wolber , Xiangyang Zhou
发明人： Jayati Ghosh , Bill Peck , Eric Leproust , Charles Troup , Glenda Delenstarr , Patrick Collins , John Corson , Paul Wolber , Xiangyang Zhou
IPC分类号： G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G06F19/24 , G06F19/20
摘要： A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the microarray data set. Spatial-intensity trends within the microarray data set are quantified, based on the surface to the intensities for each channel of the microarray data set. After the surface has been determined, the spatial-intensity trend can be removed from the microarray data set.
摘要翻译：一种用于量化和校正具有一个或多个通道的微阵列数据集的每个通道的空间强度趋势的方法和系统。本发明的一个实施例的方法和系统从微阵列数据集的每个通道中选择一组特征。基于所选择的特征集合，使用表面来确定微阵列数据集的每个通道中的所有特征的强度。基于微阵列数据集的每个通道的表面到强度，量化微阵列数据集内的空间强度趋势。在确定表面之后，可以从微阵列数据集中去除空间强度趋势。

2. 发明申请

US20050027461A1 Methods for evaluating oligonucleotide probe sequences 审中-公开
标题翻译：评估寡核苷酸探针序列的方法
公开(公告)号：US20050027461A1
公开(公告)日：2005-02-03
申请号：US10877231
申请日：2004-06-24
申请人： Karen Shannon , Paul Wolber , Glenda Delenstarr , Peter Webb , Robert Kincaid
发明人： Karen Shannon , Paul Wolber , Glenda Delenstarr , Peter Webb , Robert Kincaid
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/20 , G06F19/24 , G06F19/00
CPC分类号： G16B25/00 , G16B40/00
摘要： Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.
摘要翻译：公开了用于预测寡核苷酸与靶核苷酸序列杂交的潜力的方法。鉴定出预定数量的唯一寡核苷酸。选择独特的寡核苷酸来对可与靶核苷酸序列杂交的核苷酸序列的整个长度进行采样。确定并评估每种上述寡核苷酸的至少一个独立地预测该组寡核苷酸与靶核苷酸序列杂交的能力的参数。基于参数的评估来鉴定预定数量的唯一寡核苷酸内的寡核苷酸的子集。鉴定了亚群中的寡核苷酸，其沿着与靶核苷酸序列可杂交的核苷酸序列的区域聚集。该方法可以借助于计算机进行。

3. 发明申请

US20050095596A1 Methods for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays 审中-公开
标题翻译：用于鉴定用于核酸阵列的合适的核酸探针序列的方法
公开(公告)号：US20050095596A1
公开(公告)日：2005-05-05
申请号：US10698195
申请日：2003-10-30
申请人： Eric Leproust , Paul Wolber
发明人： Eric Leproust , Paul Wolber
IPC分类号： B01J19/00 , C12Q1/68 , C40B40/06 , C40B50/14 , C40B70/00
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00549 , B01J2219/00659 , B01J2219/00675 , B01J2219/00693 , B01J2219/00722 , C12Q1/6837 , C40B40/06 , C40B50/14 , C40B70/00
摘要： Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, for use as a surface immobilized probe for a target molecule of interest, e.g., a target nucleic acid, are provided. A feature of the subject methods is that a set of candidate sequences is evaluated for full-length synthesis probability, e.g., by evaluating the candidate sequences' depurination susceptibility. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.
摘要翻译：提供了鉴定探针例如生物聚合物探针（例如核酸）的序列用于靶目标分子例如目标核酸的表面固定化探针的方法。本发明方法的一个特征是，例如通过评估候选序列的去毒敏感性来评估一组候选序列的全长合成概率。本发明还包括用于执行记录在计算机可读介质上的主题方法的算法，以及包括其的计算分析系统。还提供了由具有由本发明方法鉴定的序列的探针产生的核酸阵列，以及使用该序列的方法。

4. 发明申请

US20050019786A1 Methods and apparatus for preparing arrays comprising features having degenerate biopolymers 失效
标题翻译：用于制备包括具有简并生物聚合物的特征的阵列的方法和装置
公开(公告)号：US20050019786A1
公开(公告)日：2005-01-27
申请号：US10722155
申请日：2003-11-25
申请人： Theodore Sana , Eric Leproust , Paul Wolber
发明人： Theodore Sana , Eric Leproust , Paul Wolber
IPC分类号： C12Q1/68 , C12P19/34 , C12P21/06
CPC分类号： C12Q1/6813
摘要： Methods and apparatus are disclosed for synthesizing a plurality of biopolymers at predetermined feature locations on a surface of a substrate. One or more of the feature locations comprises degenerate biopolymers. One or more biopolymer subunit precursors are added, in multiple rounds of subunit additions, at each of multiple feature locations on the surface to form the plurality of biopolymers on the surface. For each feature location comprising degenerate biopolymers, the biopolymer subunit precursors comprise a mixture of biopolymer subunit precursors for forming the degenerate biopolymers at the feature location.
摘要翻译：公开了用于在基材表面上的预定特征位置合成多种生物聚合物的方法和装置。一个或多个特征位置包括简并生物聚合物。在表面上的多个特征位置的每一个处，在多轮亚基添加物中加入一种或多种生物聚合物亚基前体，以在表面上形成多种生物聚合物。对于包含简并生物聚合物的每个特征位置，生物聚合物亚基前体包含用于在特征位置形成简并生物聚合物的生物聚合物亚基前体的混合物。

5. 发明申请

US20050148004A1 Chemical arrays and methods of using the same 失效
标题翻译：化学数组及其使用方法
公开(公告)号：US20050148004A1
公开(公告)日：2005-07-07
申请号：US11008603
申请日：2004-12-08
申请人： Paul Wolber , Robert Kincaid , Douglas Amorese , Diane Ilsley-Tyree , Andrew Atwell , Mel Kronick , Eric Leproust
发明人： Paul Wolber , Robert Kincaid , Douglas Amorese , Diane Ilsley-Tyree , Andrew Atwell , Mel Kronick , Eric Leproust
IPC分类号： B01J19/00 , C12Q1/68 , C40B40/06 , C40B70/00 , C12P19/34
CPC分类号： C12Q1/6883 , B01J2219/00497 , B01J2219/00572 , B01J2219/00574 , B01J2219/00576 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00617 , B01J2219/00626 , B01J2219/00659 , B01J2219/00675 , B01J2219/00722 , B82Y30/00 , C12Q1/6806 , C12Q1/6837 , C12Q1/6876 , C12Q2600/158 , C40B40/06 , C40B50/14 , C40B70/00 , C12Q2565/537 , C12Q2525/161 , C12Q2565/525 , C12Q2525/131 , C12Q2521/301
摘要： Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.
摘要翻译：提供了从初始化学阵列产生产物分子的混合物的方法和组合物。在本发明方法中，表面固定的第一部分的化学阵列经受切割条件，使得产生溶液相第一部分的组合物。然后将所得到的溶液相第一部分的组合物与一种或多种反应物接触以产生不同于第一部分的产物分子的混合物。还提供了用于实践本发明方法的主题方法和试剂盒中使用的阵列。

6. 发明申请

US20050095598A1 Nucleic acid arrays comprising depurination probe features and methods for using the same 审中-公开
标题翻译：包含脱嘌呤探针特征的核酸阵列及其使用方法
公开(公告)号：US20050095598A1
公开(公告)日：2005-05-05
申请号：US10699281
申请日：2003-10-30
申请人： Paul Wolber , Eric Leproust
发明人： Paul Wolber , Eric Leproust
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00626 , B01J2219/00722 , C12Q2545/101
摘要： In situ produced nucleic acid arrays that include at least one depurination probe feature are provided, where the at least one depurination probe feature is made up of in situ produced depurination probes. In using the subject arrays, the arrays are contacted with a nucleic acid sample that includes a target which specifically binds to the full length depurination probe of the depurination feature, and the amount of resultant duplex nucleic acids in the feature is determined (e.g., based on detected signal from the feature) to evaluate the extent of depurination that occurred during in situ synthesis of the array. The subject arrays find use in a variety of different applications, including array fabrication quality control applications, e.g., to determine the extent of depurination in a given lot of nucleic acid arrays produced using an in situ fabrication protocol. Also provided are computer programming, devices that include the same and kits that find use in practicing the subject methods.
摘要翻译：提供了包含至少一个去除血清探针特征的原位产生的核酸阵列，其中至少一个去血清探针特征由原位产生的去血清探针组成。在使用受试者阵列时，使阵列与核酸样品接触，所述核酸样品包括特异性结合脱嘌呤特征的全长去除探针的靶标，并且确定特征中得到的双链体核酸的量（例如，基于对来自特征的检测信号）来评估在阵列的原位合成期间发生的去除程度。主题阵列可用于各种不同的应用，包括阵列制造质量控制应用，例如确定使用原位制备方案产生的给定批次的核酸阵列中的去除程度。还提供了计算机程序设计，包括相同的设备和用于实践主题方法的套件。

7. 发明申请

US20050244885A1 Array based methods for synthesizing nucleic acid mixtures 审中-公开
标题翻译：用于合成核酸混合物的基于阵列的方法
公开(公告)号：US20050244885A1
公开(公告)日：2005-11-03
申请号：US11174042
申请日：2005-07-01
申请人： Paul Wolber , Robert Kincaid , Douglas Amorese , Diane Ilsley , Andrew Atwell
发明人： Paul Wolber , Robert Kincaid , Douglas Amorese , Diane Ilsley , Andrew Atwell
IPC分类号： B01J19/00 , C12Q1/68 , C40B40/06 , C40B70/00 , C12P19/34
CPC分类号： C12Q1/6883 , B01J2219/00497 , B01J2219/00572 , B01J2219/00574 , B01J2219/00576 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00617 , B01J2219/00626 , B01J2219/00659 , B01J2219/00675 , B01J2219/00722 , B82Y30/00 , C12Q1/6806 , C12Q1/6837 , C12Q1/6876 , C12Q2600/158 , C40B40/06 , C40B50/14 , C40B70/00 , C12Q2565/537 , C12Q2525/161 , C12Q2565/525 , C12Q2525/131 , C12Q2521/301
摘要： Methods for generating mixtures of nucleic acids, e.g., oligonucleotide primers, are provided. In the subject methods, an array is employed as template to generate mixtures of nucleic acids via a template driven primer extension reaction. In preferred embodiments, each probe on the array employed in the subject methods comprises a constant domain and a variable domain, where the constant domain is further characterized by having at least a recognition domain. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods. The subject methods find use in a variety of applications, including the generation of target nucleic acids from an mRNA sample for use in hybridization assays, e.g., differential gene expression analyses.
摘要翻译：提供了产生核酸混合物的方法，例如寡核苷酸引物。在主题方法中，使用阵列作为模板，以通过模板驱动的引物延伸反应产生核酸的混合物。在优选实施方案中，在本方法中使用的阵列上的每个探针包括恒定结构域和可变结构域，其中恒定结构域的进一步特征在于至少具有识别结构域。还提供了用于实践本发明方法的主题方法和试剂盒中使用的阵列。本发明方法可用于各种应用，包括从用于杂交测定的mRNA样品中产生靶核酸，例如差异基因表达分析。

8. 发明申请

US20050026154A1 Masking chemical arrays 审中-公开
标题翻译：掩蔽化学阵列
公开(公告)号：US20050026154A1
公开(公告)日：2005-02-03
申请号：US10633609
申请日：2003-07-31
申请人： Laurakay Bruhn , Douglas Amorese , Michael Caren , Leslie Leonard , Richard Pittaro , Carol Schembri , Peter Webb , Paul Wolber
发明人： Laurakay Bruhn , Douglas Amorese , Michael Caren , Leslie Leonard , Richard Pittaro , Carol Schembri , Peter Webb , Paul Wolber
IPC分类号： B01J19/00 , B01L3/00 , C12Q1/68 , C40B40/06 , G01N21/25 , G01N33/48 , G01N33/483 , G01N33/50 , G01N33/53 , G01N33/58 , G06F19/00
CPC分类号： B01L3/545 , B01J2219/00662 , B01J2219/00693 , B01J2219/00722 , B01L3/5088 , B01L2200/025 , B01L2300/024 , B01L2300/0819 , C40B40/06 , G01N21/253
摘要： A method of using a chemical array unit having a chemical array with probes at multiple feature locations. A request for test may be read, which test uses a sub-array of the array. A pattern of the sub-array may be retrieved from a memory using the test request, which memory carries a pattern for the sub-array which is retrievable with the different test request. Also, a method of reading a chemical array unit which has been exposed to a sample, and feature locations of which have been rendered incapable of providing signal data representative of binding of a sample component. Further methods, apparatus, and computer program products are provided.
摘要翻译：一种在多个特征位置使用具有化学阵列的化学阵列单元和探针的方法。可以读取测试请求，哪个测试使用数组的子阵列。可以使用测试请求从存储器检索子阵列的模式，该存储器携带用于使用不同测试请求可检索的子阵列的模式。此外，读取已经暴露于样品的化学阵列单元的方法，其特征位置已经不能提供表示样品组分的结合的信号数据。提供其他方法，装置和计算机程序产品。

9. 发明申请

US20060073486A1 Multiple array substrates and methods for using the same 审中-公开
标题翻译：多阵列基板及其使用方法
公开(公告)号：US20060073486A1
公开(公告)日：2006-04-06
申请号：US10957062
申请日：2004-10-01
申请人： Theodore Sana , Paul Wolber
发明人： Theodore Sana , Paul Wolber
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6837 , C12Q2545/101 , C12Q2525/161
摘要： Multiple array substrates and methods for their use are provided. A feature of aspects of the invention is that the arrays of the multiple array substrate include a control set of probe nucleic acids that provides for the opportunity to screen for at least one of cross contamination among arrays and a probe synthesis error. Also provided are kits for practicing various aspects of the invention.
摘要翻译：提供了多种阵列基板及其使用方法。本发明的方面的特征在于，多阵列衬底的阵列包括探针核酸的对照组，其提供筛选阵列之间的交叉污染中的至少一种和探针合成误差的机会。还提供了用于实践本发明的各个方面的套件。

10. 发明申请

US20050136427A1 Methods for controlling cross-hybridization in analysis of nucleic acid sequences 审中-公开
标题翻译：在核酸序列分析中控制交叉杂交的方法
公开(公告)号：US20050136427A1
公开(公告)日：2005-06-23
申请号：US10877159
申请日：2004-06-24
申请人： Paul Wolber , Robert Kincaid
发明人： Paul Wolber , Robert Kincaid
IPC分类号： C12Q1/68 , B05D3/00 , C12M1/34 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： C12Q1/6813
摘要： Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.
摘要翻译：公开了用于选择可用于分析靶核酸序列的靶特异性寡核苷酸探针的方法，试剂和试剂盒。一方面，本发明涉及选择一组靶特异性寡核苷酸探针。基于目标核酸序列的候选靶特异性寡核苷酸探针鉴定交叉杂交寡核苷酸探针。交叉杂交寡核苷酸探针测量具有预定概率的交叉杂交事件的发生程度。使用交叉杂交寡核苷酸探针和靶特异性寡核苷酸探针测定交叉杂交结果。基于交叉杂交结果，针对该组选择或拒绝靶特异性寡核苷酸探针。

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