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    Method for Fragmenting Genomic DNA Using CAS9
    11.
    发明申请
    Method for Fragmenting Genomic DNA Using CAS9 审中-公开

    公开(公告)号：US20200172959A1

    公开(公告)日：2020-06-04

    申请号：US16748267

    申请日：2020-01-21

    Applicant: AGILENT TECHNOLOGIES, INC.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Michael Walter ,  Bram Herman

    IPC: C12Q1/6806 ,  C12N9/22 ,  C12Q1/6869 ,  C12N15/10

    Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

    Method for fragmenting genomic DNA using CAS9
    12.
    发明授权
    Method for fragmenting genomic DNA using CAS9 有权

    公开(公告)号：US10577644B2

    公开(公告)日：2020-03-03

    申请号：US15339510

    申请日：2016-10-31

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Michael Walter ,  Bram Herman

    IPC: C12Q1/6806 ,  C12N15/11 ,  C12Q1/68 ,  C12P19/34 ,  C12N15/10 ,  C12Q1/6869 ,  C12N9/22

    Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

    Isolation of RNA-protein complexes using cross-linking reagents and oligonucleotides
    15.
    发明授权
    Isolation of RNA-protein complexes using cross-linking reagents and oligonucleotides 有权
    使用交联试剂和寡核苷酸分离RNA蛋白复合物

    公开(公告)号：US09574236B2

    公开(公告)日：2017-02-21

    申请号：US14590869

    申请日：2015-01-06

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Phillip Smart ,  Robert A. Ach

    IPC: G01N33/68 ,  C12Q1/68 ,  G01N33/53

    CPC classification number: C12Q1/6876 ,  C12Q1/6844 ,  C12Q2600/158 ,  C12Q2600/178 ,  G01N33/5308 ,  G01N33/6803 ,  G01N33/6848 ,  Y10T436/143333

    Abstract: Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided.

    Abstract translation: 本文提供了一种样品分析方法。 在某些实施方案中，所述方法包括：a）使用第一化合物交联细胞的蛋白质以产生包含交联蛋白质和RNA的第一交联产物; b）在第二化合物的寡核苷酸部分与RNA杂交的条件下使第一交联产物和第二化合物接触; c）使第一和第二化合物活化反应，由此共价交联寡核苷酸与交联蛋白质以产生第二交联产物; d）使用亲和标签分离第二交联产物; 和e）分析分离的第二交联产物。 还提供了用于执行该方法的化合物。

    METHOD FOR FRAGMENTING GENOMIC DNA USING CAS9
    16.
    发明申请
    METHOD FOR FRAGMENTING GENOMIC DNA USING CAS9 审中-公开
    使用CAS9分离基因组DNA的方法

    公开(公告)号：US20170044592A1

    公开(公告)日：2017-02-16

    申请号：US15339510

    申请日：2016-10-31

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Michael Walter ,  Bram Herman

    IPC: C12Q1/68

    CPC classification number: C12Q1/6806 ,  C12N9/22 ,  C12N15/1003 ,  C12N15/1034 ,  C12Q1/6869 ,  C12Y301/00 ,  Y10T436/143333

    Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

    Abstract translation: 提供了一种分割基因组的方法。 在某些实施方案中，所述方法包括：（a）将含有基因组DNA的基因组样品与多个Cas9-gRNA复合物组合，其中所述Cas9-gRNA复合物包含Cas9蛋白和至少10个Cas9相关导向RNA的集合，其中 与基因组中不同的，预定义的位点互补，以产生反应混合物; 和（b）孵育反应混合物以产生至少5个基因组DNA片段。 还提供了包含至少100种与基因组中不同的，预定义的位点互补的Cas9相关导向RNA的组合物。 还提供了用于执行该方法的套件。 此外，还提供用于操作核酸的其它方法，组合物和试剂盒。

    Nucleic acid enrichment using Cas9
    18.
    发明授权
    Nucleic acid enrichment using Cas9 有权

    公开(公告)号：US11414695B2

    公开(公告)日：2022-08-16

    申请号：US14290901

    申请日：2014-05-29

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/6806 ,  C12N9/22 ,  C12N15/10 ,  C12Q1/6869

    Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

    Spatial molecular barcoding of in situ nucleic acids
    20.
    发明授权
    Spatial molecular barcoding of in situ nucleic acids 有权

    公开(公告)号：US09834814B2

    公开(公告)日：2017-12-05

    申请号：US14493127

    申请日：2014-09-22

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Alicia Scheffer-Wong ,  Carolina Caffaro

    IPC: C12Q1/68 ,  G01N33/53 ,  C07H21/00

    CPC classification number: C12Q1/6841 ,  C12Q2565/513 ,  C12Q2565/514

    Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.

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