ChIP-seq/ChIP-qPCR プロファイリングサービス

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  •  資料
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Catalog Number


  • 経験と実績:IHEC-BLUEPRINT Epigenome Consortiaの公式パートナーであり、ChIP-seqにおける10年の実績と経験

  • カスタマイズ可能なサポートプラン

  • 専門チームによるプロジェクト調整
  • ENCODE標準の高品質データ

ChIPは複雑で難しいという印象が強いですが、適切なツールがあれば確実な実験ができます。 ChIPの原理は、実は単純で特異的抗原を含むクロマチン画分の選択的濃縮と関係します。 目的のタンパク質またはタンパク質修飾を認識する抗体を使用することで、in vivoでゲノムの1つまたは複数の位置で、その抗原の相対的存在量を決定できます。

  • 詳細

    In order to provide you with the highest quality data, our ChIP-seq service is composed of two major steps:

    1. ChIP validation - during this step we optimize the ChIP conditions that depend on your sample type, target and amount of cells.
    2. ChIP on sample of interest - once the best ChIP conditions are validated, the samples of interest can be processed.

    ChIP-seq service includes:

    1. ChIP validation Chromatin Shearing validation
    • Testing 2 shearing times for each cell type/tissue type
    ChIP/Ab validation
    • Testing 2 Ab amounts and/or 2 Ab references per target of interest
    • qPCR analysis if positive and negative control regions can be provided
    • Library preparation on IPs and INPUTs material
    • Illumina sequencing run : Paired-end reads, 2x 50 bp, sequencing depth will be adjusted depending on the mark/specie studied
    • Quality check, alignment to reference genome, identification of enriched regions (peak calling)
    Primers design and validation
    • Performed on gDNA based on the data obtained during the ChIP/Ab validation. Those primers will be used for further qPCR validation of the ChIP on the samples of interest
    2. ChIP on sample of interest Chromatin IP
    • Chromatin shearing
    • IPs
    • qPCR analysis using primers that have been validated during the ChIP validation
    Library Preparation
    • Library preparation and purification on IPs and INPUTs material
    • Illumina sequencing run: Paired-end reads, 2x 50 bp, sequencing depth will be adjusted depending on the mark/specie studied
  • バイオインフォマティック解析

    Bioinformatic analyses on samples of interest

    Standard bioinformatics

    • Quality check, alignment to reference genome, identification of enriched regions (peak calling)
    Advanced bioinformatics

    Differential binding analysis

    • Identification and annotation of differential binding sites between samples based on previously identified ChIP-seq peaks
    Annotation in genomic regions
    • Annotation of ChIP-seq peaks with genomic regions: introns, exons, promoters, 1-to-5 kb upstream-TSS and intergenic regions
    Gene ontology termes analysis
    • Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in bound regions or differentially bound regions may indicate the underlying biological processes involved
    Pathway analysis
    • Identify biochemical pathways in which genes associated with bound regions or differentially bound regions may be overrepresented
    Visualization of specific genomic regions
    • Visualization of results (i.e. sequencing data, peaks) at specific genomic regions (e.g. genes, promoters) in publication-ready images
  •  資料
    Epigenomics Profiling Services FLYER
    Chromatin analysis DNA methylation services RNA-seq analysis
  •  出版物

    How to properly cite this product in your work

    Diagenode strongly recommends using this: ChIP-seq/ChIP-qPCR プロファイリングサービス (Diagenode Cat# G02010000). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Impact of Fetal Exposure to Endocrine Disrupting ChemicalMixtures on FOXA3 Gene and Protein Expression in Adult RatTestes.
    Walker C. et al.
    Perinatal exposure to endocrine disrupting chemicals (EDCs) has been shown to affect male reproductive functions. However, the effects on male reproduction of exposure to EDC mixtures at doses relevant to humans have not been fully characterized. In previous studies, we found that in utero exposure to mixtures of th...

    Histone Deacetylases 1 and 2 target gene regulatory networks of nephronprogenitors to control nephrogenesis.
    Liu Hongbing et al.
    Our studies demonstrated the critical role of Histone deacetylases (HDACs) in the regulation of nephrogenesis. To better understand the key pathways regulated by HDAC1/2 in early nephrogenesis, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) of Hdac1/2 on isolated nephron progenitor cells (NPCs) fro...

    Identification of genomic binding sites and direct target genes for thetranscription factor DDIT3/CHOP.
    Osman A. et al.
    DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene...

    CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells.
    Bommi-Reddy A. et al.
    Therapeutic targeting of the estrogen receptor (ER) is a clinically validated approach for estrogen receptor positive breast cancer (ER+ BC), but sustained response is limited by acquired resistance. Targeting the transcriptional coactivators required for estrogen receptor activity represents an alternative approach...

    Epigenetic regulation of the lineage specificity of primary human dermallymphatic and blood vascular endothelial cells.
    Tacconi, Carlotta and He, Yuliang and Ducoli, Luca and Detmar, Michael
    Lymphatic and blood vascular endothelial cells (ECs) share several molecular and developmental features. However, these two cell types possess distinct phenotypic signatures, reflecting their different biological functions. Despite significant advances in elucidating how the specification of lymphatic and blood vasc...

    Battle of the sex chromosomes: competition between X- and Y-chromosomeencoded proteins for partner interaction and chromatin occupancy drivesmulti-copy gene expression and evolution in muroid rodents.
    Moretti, C and Blanco, M and Ialy-Radio, C and Serrentino, ME and Gobé,C and Friedman, R and Battail, C and Leduc, M and Ward, MA and Vaiman, Dand Tores, F and Cocquet, J
    Transmission distorters (TDs) are genetic elements that favor their own transmission to the detriments of others. Slx/Slxl1 (Sycp3-like-X-linked and Slx-like1) and Sly (Sycp3-like-Y-linked) are TDs which have been co-amplified on the X and Y chromosomes of Mus species. They are involved in an intragenomic conflict i...

    Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes.
    Crespo M, Damont A, Blanco M, Lastrucci E, Kennani SE, Ialy-Radio C, Khattabi LE, Terrier S, Louwagie M, Kieffer-Jaquinod S, Hesse AM, Bruley C, Chantalat S, Govin J, Fenaille F, Battail C, Cocquet J, Pflieger D
    Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and ...

    A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex.
    Kvist J, Athanàsio CG, Pfrender ME, Brown JB, Colbourne JK, Mirbahai L
    BACKGROUND: Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large difference...

    Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq.
    Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR
    One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me...

    Development and epigenetic plasticity of murine Müller glia.
    Dvoriantchikova G, Seemungal RJ, Ivanov D
    The ability to regenerate the entire retina and restore lost sight after injury is found in some species and relies mostly on the epigenetic plasticity of Müller glia. To understand the role of mammalian Müller glia as a source of progenitors for retinal regeneration, we investigated changes in gene expres...

    The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue.
    Dvoriantchikova G, Seemungal RJ, Ivanov D
    The epigenetic plasticity of amphibian retinal pigment epithelium (RPE) allows them to regenerate the entire retina, a trait known to be absent in mammals. In this study, we investigated the epigenetic plasticity of adult murine RPE to identify possible mechanisms that prevent mammalian RPE from regenerating retinal...

    Epigenetic modifiers promote mitochondrial biogenesis and oxidative metabolism leading to enhanced differentiation of neuroprogenitor cells.
    Martine Uittenbogaard, Christine A. Brantner, Anne Chiaramello1
    During neural development, epigenetic modulation of chromatin acetylation is part of a dynamic, sequential and critical process to steer the fate of multipotent neural progenitors toward a specific lineage. Pan-HDAC inhibitors (HDCis) trigger neuronal differentiation by generating an "acetylation" signature and prom...

    The epigenetic architecture at gene promoters determines cell type-specific LPS tolerance
    Kerstin Klein , Mojca Frank-Bertoncelj , Emmanuel Karouzakis , Renate E. Gay , Christoph Kolling , Adrian Ciurea , Nagihan Bostanci , Georgios N. Belibasakis , Lih-Ling Lin , Oliver Distler , Steffen Gay , Caroline Ospelt
    Synovial fibroblasts (SF) drive inflammation and joint destruction in chronic arthritis. Here we show that SF possess a distinct type of LPS tolerance compared to macrophages and other types of fibroblasts. In SF and dermal fibroblasts, genes that were non-tolerizable after repeated LPS stimulation included proinfla...

    PPARγ Links BMP2 and TGFβ1 Pathways in Vascular Smooth Muscle Cells, Regulating Cell Proliferation and Glucose Metabolism
    Laurent Calvier, Philippe Chouvarine, Ekaterina Legchenko, Nadine Hoffmann, Jonas Geldner, Paul Borchert, Danny Jonigk, Miklos M. Mozes, Georg Hansmann
    BMP2 and TGFβ1 are functional antagonists of pathological remodeling in the arteries, heart, and lung; however, the mechanisms in VSMCs, and their disturbance in pulmonary arterial hypertension (PAH), are unclear. We found a pro-proliferative TGFβ1-Stat3-FoxO1 axis in VSMCs, and PPARγ as in...

    Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions
    Mojca Frank-Bertoncelj, Michelle Trenkmann, Kerstin Klein, Emmanuel Karouzakis, Hubert Rehrauer, Anna Bratus, Christoph Kolling, Maria Armaka, Andrew Filer, Beat Michel, Renate E. Gay, Christopher D. Buckley, George Kollias, Steffen Gay & Caroline Ospelt
    A number of human diseases, such as arthritis and atherosclerosis, include characteristic pathology in specific anatomical locations. Here we show transcriptomic differences in synovial fibroblasts from different joint locations and that HOX gene signatures reflect the joint-specific origins of mouse and human synov...

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