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ctcf chip-seq data  (Epigenomics ag)

 
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    Epigenomics ag ctcf chip-seq data
    Ctcf Chip Seq Data, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ctcf+chip-seq+data/ctcf+chip+seq/pmc08007156-200-22-31
    Average 90 stars, based on 1 article reviews
    ctcf chip-seq data - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Chromatin Immunoprecipitation:

    Article Title: Bromodomain protein BRD4 is an epigenetic activator of B7-H6 expression in acute myeloid leukemia
    Article Snippet: This region is considered an enhancer-like by Registry of candidate cis-Regulatory Elements (cCREs) of ENCODE, which integrates DNase-seq and H3K4me3, H3K27ac, and CTCF ChIP-seq data produced by the ENCODE and Roadmap Epigenomics Consortia.

    Article Title: Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
    Article Snippet: Type 4: CTCF ChIP-seq peaks outside loop anchors within DNase hypersensitive regions: In order to compare loop-anchor CTCF sites to non-loop anchor CTCF sites, we selected CTCF sites from the latter category within the top 100 TADs containing growth genes subject to the requirement that they overlap K562 DNase hypersensitive regions from the Roadmap Epigenomics data from the University of Washington 16.

    Article Title: A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers.
    Article Snippet: Somatic mutations drive cancer and there are established ways to study those in coding sequences.. It has been shown that some regulatory mutations are overrepresented in cancer.. We develop a new strategy to find putative regulatory mutations based on experimentally established motifs for transcription factors (TFs).

    Produced:

    Article Title: Bromodomain protein BRD4 is an epigenetic activator of B7-H6 expression in acute myeloid leukemia
    Article Snippet: This region is considered an enhancer-like by Registry of candidate cis-Regulatory Elements (cCREs) of ENCODE, which integrates DNase-seq and H3K4me3, H3K27ac, and CTCF ChIP-seq data produced by the ENCODE and Roadmap Epigenomics Consortia.

    Article Title: Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
    Article Snippet: Type 4: CTCF ChIP-seq peaks outside loop anchors within DNase hypersensitive regions: In order to compare loop-anchor CTCF sites to non-loop anchor CTCF sites, we selected CTCF sites from the latter category within the top 100 TADs containing growth genes subject to the requirement that they overlap K562 DNase hypersensitive regions from the Roadmap Epigenomics data from the University of Washington 16.

    Article Title: A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers.
    Article Snippet: Somatic mutations drive cancer and there are established ways to study those in coding sequences.. It has been shown that some regulatory mutations are overrepresented in cancer.. We develop a new strategy to find putative regulatory mutations based on experimentally established motifs for transcription factors (TFs).



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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    ctcf chip-seq data  (Epigenomics ag)
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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    ctcf chip-seq data  (Broad Institute Inc)
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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    ctcf chip-seq data sets  (Broad Institute Inc)
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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    ctcf chip seq data  (Cell Signaling Technology Inc)
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    Chrom-Sig results on <t>GM12878</t> CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.
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    chip-seq data for ctcf  (Santa Cruz Biotechnology)
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    Chromatin 3D structures. Shown is a two-dimensional heatmap of Hi-C interaction frequencies in IMR90 cells from a 5 MB region of Chr2 generated using the website: http://www.3dgenome.org and the color key represents the interaction counts between two loci. Highlighted in gray is a repressed compartment and highlighted in orange is an active compartment. Also shown <t>is</t> <t>ChIP-seq</t> data for <t>CTCF</t> and histone modifications, as well as a wavelet-smoothed Repli-seq track representing DNA replication timing; all datasets were taken from the University of California, Santa Cruz genome browser. For each compartment, a model of chromatin interactions is shown (which are more frequent within a TAD than between TADs) facilitated by CTCF, Cohesin, and Mediator. Long-distance constitutive interactions require a pair of CTCF sites with convergently orientated motifs as anchors; any combination of CTCF, cohesin, and mediator can facilitate median distance interactions. Many other CTCF-binding sites (green bars) are not involved in chromatin interactions and occur within loops. (see the color version of this figure at www.informahealthcare.com/bmg ).
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    Image Search Results


    Chrom-Sig results on GM12878 CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.

    Journal: Bioinformatics

    Article Title: Chrom-Sig: de-noising 1D genomic profiles by signal processing methods

    doi: 10.1093/bioinformatics/btaf645

    Figure Lengend Snippet: Chrom-Sig results on GM12878 CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.

    Article Snippet: For example, the GM12878 CTCF ChIP-seq data were originally noisy with a large portion of reads in non-binding sites, but Chrom-Sig with FDR of 0.1 retained only the reads with strong binding ( ).

    Techniques: ChIP-sequencing, Binding Assay, Generated

    Chromatin 3D structures. Shown is a two-dimensional heatmap of Hi-C interaction frequencies in IMR90 cells from a 5 MB region of Chr2 generated using the website: http://www.3dgenome.org and the color key represents the interaction counts between two loci. Highlighted in gray is a repressed compartment and highlighted in orange is an active compartment. Also shown is ChIP-seq data for CTCF and histone modifications, as well as a wavelet-smoothed Repli-seq track representing DNA replication timing; all datasets were taken from the University of California, Santa Cruz genome browser. For each compartment, a model of chromatin interactions is shown (which are more frequent within a TAD than between TADs) facilitated by CTCF, Cohesin, and Mediator. Long-distance constitutive interactions require a pair of CTCF sites with convergently orientated motifs as anchors; any combination of CTCF, cohesin, and mediator can facilitate median distance interactions. Many other CTCF-binding sites (green bars) are not involved in chromatin interactions and occur within loops. (see the color version of this figure at www.informahealthcare.com/bmg ).

    Journal: Critical Reviews in Biochemistry and Molecular Biology

    Article Title: Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

    doi: 10.3109/10409238.2015.1087961

    Figure Lengend Snippet: Chromatin 3D structures. Shown is a two-dimensional heatmap of Hi-C interaction frequencies in IMR90 cells from a 5 MB region of Chr2 generated using the website: http://www.3dgenome.org and the color key represents the interaction counts between two loci. Highlighted in gray is a repressed compartment and highlighted in orange is an active compartment. Also shown is ChIP-seq data for CTCF and histone modifications, as well as a wavelet-smoothed Repli-seq track representing DNA replication timing; all datasets were taken from the University of California, Santa Cruz genome browser. For each compartment, a model of chromatin interactions is shown (which are more frequent within a TAD than between TADs) facilitated by CTCF, Cohesin, and Mediator. Long-distance constitutive interactions require a pair of CTCF sites with convergently orientated motifs as anchors; any combination of CTCF, cohesin, and mediator can facilitate median distance interactions. Many other CTCF-binding sites (green bars) are not involved in chromatin interactions and occur within loops. (see the color version of this figure at www.informahealthcare.com/bmg ).

    Article Snippet: Also shown is ChIP-seq data for CTCF and histone modifications, as well as a wavelet-smoothed Repli-seq track representing DNA replication timing; all datasets were taken from the University of California, Santa Cruz genome browser.

    Techniques: Hi-C, Generated, ChIP-sequencing, Binding Assay