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    GENOME-SCALE IMAGING OF THE 3D ORGANIZATION AND TRANSCRIPTIONAL ACTIVITY OF CHROMATIN
    31.
    发明公开
    GENOME-SCALE IMAGING OF THE 3D ORGANIZATION AND TRANSCRIPTIONAL ACTIVITY OF CHROMATIN 审中-公开

    公开(公告)号：US20230348958A1

    公开(公告)日：2023-11-02

    申请号：US17770943

    申请日：2020-12-18

    申请人： President and Fellows of Harvard College

    发明人： Xiaowei Zhuang ,  Bogdan Bintu ,  Seon S. Kinrot ,  Pu Zheng ,  Jun-Han Su

    IPC分类号： C12Q1/6841 ,  G16B40/10 ,  G16B15/10

    CPC分类号： C12Q1/6841 ,  G16B40/10 ,  G16B15/10 ,  C12Q2600/16

    摘要： The present invention generally relates to genomics. Some embodiments are directed to imaging the 3D organization of the genome, or part of the genome, with high throughput in the sequence space. Some embodiments are directed to imaging the 3D organization of the genome, or part of the genome, in the context of transcriptional activity and nuclear structures. In addition, certain embodiments are directed to chromatin structures, 3D chromatin organizations, trans-chromosomal interactions and chromatin-nuclear-structure interactions as well as their relationship with transcription, etc. In addition, various embodiments are directed to imaging methods that allow mapping of the 3D organization of the genome, or part of the genome, in the context of nuclear structures and transcriptional activity. Some embodiments are directed to massively multiplexed fluorescence in situ hybridization methods for imaging chromatin loci and/or nascent RNA transcripts at the chromosome or genome scale.

    IMPROVED HIGH EFFICIENCY TARGETED IN SITU GENOME-WIDE PROFILING
    34.
    发明公开
    IMPROVED HIGH EFFICIENCY TARGETED IN SITU GENOME-WIDE PROFILING 审中-公开

    公开(公告)号：US20230332213A1

    公开(公告)日：2023-10-19

    申请号：US18044289

    申请日：2021-09-10

    申请人： Fred Hutchinson Cancer Center

    发明人： Steven Henikoff

    IPC分类号： C12Q1/6841 ,  C12Q1/6858

    CPC分类号： C12Q1/6841 ,  C12Q1/6858 ,  C12Q2600/166 ,  C12Q1/6806

    摘要： The disclosure provides methods and related systems and reagents for detecting, sequencing, and/or mapping sites of DNA accessibility in the chromatin of a cell. The method comprises contacting a permeabilized cells with an affinity reagent that specifically binds a nucleosome depleted region (NDR) marker. The first affinity reagent is coupled, directly or indirectly, with at least one transposome. The transposase component of the transposome is activated under low ionic conditions, resulting in cleaving and tagging chromatin DNA. The DNA segment, thus tagged, is excised by virtue of multiple cleavage points, which is then isolated for analysis (e.g., sequencing and mapping). The method can include additional affinity reagents that are similarly functionalized but instead bind to negative regulatory elements in the chromatin, thus allowing for the simultaneous mapping of DNA accessibility and inaccessibility in the genome of a single cell. The methods can be applied to a variety of analytic platforms.

    METHOD COMBINING IN SITU TARGET CAPTURE AND SPATIAL UNIQUE MOLECULAR IDENTIFIER (SUMI) IDENTIFICATION WITH IN VITRO SEQUENCING FOR HIGH DENSITY SPATIAL MULTIOMICS
    36.
    发明公开
    METHOD COMBINING IN SITU TARGET CAPTURE AND SPATIAL UNIQUE MOLECULAR IDENTIFIER (SUMI) IDENTIFICATION WITH IN VITRO SEQUENCING FOR HIGH DENSITY SPATIAL MULTIOMICS 审中-公开

    公开(公告)号：US20230323438A1

    公开(公告)日：2023-10-12

    申请号：US18131128

    申请日：2023-04-05

    申请人： Miltenyi Biotec B.V. & Co. KG

    发明人： Thomas Rothmann ,  Robert Pinard ,  Seiyu Hosono ,  Andreas Bosio

    IPC分类号： C12Q1/6841

    CPC分类号： C12Q1/6841

    摘要： Microscopy imaging that allow for multiple mRNAs, proteins and metabolites to be spatially resolved at a subcellular level provides valuable molecular information which is a crucial factor for understanding tissue heterogeneity as for example within the tumor micro environment. The current invention describes a method (High Density—SUMI-Seq) which combines the use of Spatial Unique Molecular Identifier in situ localization and identification (by in situ sequencing or sequential fluorescence hybridization) of rolonies derived from rolling circle amplification of circular oligonucleotides and in vitro sequencing of target captured RNA or DNA in combination with SUMI identification at a subcellular level with no optical diffraction limitation in the amount of captured target information that can be analyzed per cell. Apart from captured RNA or DNA, the High Density—SUMI-Seq method can also be applied using linear oligonucleotides to spatially resolve proteins and metabolites to provide multiomics results.