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  1. Article ; Online: Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq.

    Ma, Shaoqian / Zhang, Yongyou

    Molecular biomedicine

    2020  Volume 1, Issue 1, Page(s) 9

    Abstract: ... embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and ... Chromatin regulatory landscape plays a critical role in many disease processes and ... such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single ...

    Abstract Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
    Language English
    Publishing date 2020-10-10
    Publishing country Singapore
    Document type Journal Article ; Review
    ISSN 2662-8651
    ISSN (online) 2662-8651
    DOI 10.1186/s43556-020-00009-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

    Ma, Shaoqian / Zhang, Yongyou

    Mol Biomed

    Abstract: ... embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and ... Chromatin regulatory landscape plays a critical role in many disease processes and ... such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single ...

    Abstract Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
    Keywords covid19
    Publisher PMC
    Document type Article ; Online
    DOI 10.1186/s43556-020-00009-w
    Database COVID19

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    Inter-library loan at ZB MED

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  3. Article ; Online: Epigenomic profiling of neuroblastoma cell lines.

    Upton, Kristen / Modi, Apexa / Patel, Khushbu / Kendsersky, Nathan M / Conkrite, Karina L / Sussman, Robyn T / Way, Gregory P / Adams, Rebecca N / Sacks, Gregory I / Fortina, Paolo / Diskin, Sharon J / Maris, John M / Rokita, Jo Lynne

    Scientific data

    2020  Volume 7, Issue 1, Page(s) 116

    Abstract: ... we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN ... cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic ... we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers ...

    Abstract Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
    MeSH term(s) Cell Line, Tumor ; Chromatin/genetics ; Chromatin Immunoprecipitation ; Epigenomics ; Gene Expression Profiling ; Histones/genetics ; Humans ; N-Myc Proto-Oncogene Protein/genetics ; Neuroblastoma/genetics
    Chemical Substances Chromatin ; Histones ; MYCN protein, human ; N-Myc Proto-Oncogene Protein
    Language English
    Publishing date 2020-04-14
    Publishing country England
    Document type Dataset ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/s41597-020-0458-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Profiling chromatin regulatory landscape

    Shaoqian Ma / Yongyou Zhang

    Molecular Biomedicine, Vol 1, Iss 1, Pp 1-

    insights into the development of ChIP-seq and ATAC-seq

    2020  Volume 13

    Abstract: ... embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and ... Abstract Chromatin regulatory landscape plays a critical role in many disease processes and ... such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single ...

    Abstract Abstract Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
    Keywords Chromatin regulatory landscape ; Epigenome sequencing ; Single cell ; Developmental biology ; Medicine ; R
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Springer
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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