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    Methods for evaluating oligonucleotide probe sequences
    2.
    发明申请
    Methods for evaluating oligonucleotide probe sequences 审中-公开
    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。

    Method for linear mRNA amplification
    5.
    发明申请
    Method for linear mRNA amplification 有权

    公开(公告)号：US20060024799A1

    公开(公告)日：2006-02-02

    申请号：US11179813

    申请日：2005-07-11

    申请人： Karen Shannon

    发明人： Karen Shannon

    IPC分类号： C12P19/34

    CPC分类号： C12N15/1096 ,  C12Q1/6806 ,  C12Q1/6865 ,  C12Q2600/158 ,  C12Q2525/173 ,  C12Q2525/143 ,  C12Q2521/119 ,  C12Q2521/107

    摘要： Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.

    Methods for identifying suitable nucleic acid normalization probe sequences for use in nucleic acid arrays
    6.
    发明申请
    Methods for identifying suitable nucleic acid normalization probe sequences for use in nucleic acid arrays 审中-公开
    用于鉴定用于核酸阵列的合适的核酸归一化探针序列的方法

    公开(公告)号：US20050079509A1

    公开(公告)日：2005-04-14

    申请号：US10686092

    申请日：2003-10-14

    申请人： Karen Shannon

    发明人： Karen Shannon

    IPC分类号： C12Q1/68 ,  C40B40/06 ,  G06F19/00 ,  G01N33/48 ,  G01N33/50

    CPC分类号： G16B25/00 ,  B01J2219/007 ,  B01J2219/00722 ,  C12Q1/6837 ,  C40B40/06

    摘要： Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, that is suitable for use as a surface immobilized normalization probe on a nucleic acid array are provided. A feature of the subject methods is that a set of computationally determined initial candidate sequences are empirically evaluated to obtain functional data that is then employed to evaluate the candidate sequences for suitability as normalization probes. Sequences identified as suitable for use as normalization probes according to the subject methods are ones that do not cluster with other probes of the candidate set, exhibit high signal intensity and exhibit substantially no differential expression across a large number of samples. 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： 提供了鉴定适合用作核酸阵列上的表面固定的归一化探针的探针序列的方法，例如生物聚合物探针，例如核酸。 本发明方法的一个特征是经验地评估一组计算确定的初始候选序列，以获得随后用于评估候选序列作为归一化探针的适用性的功能数据。 根据本发明方法鉴定为适合用作归一化探针的序列是不与候选组的其他探针聚簇的序列，表现出高信号强度，并且在大量样品上基本上不显示差异表达。 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。