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gm12878 ctcf chip seq data  (Chrom Tech)

 
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    Chrom Tech gm12878 ctcf chip seq data
    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.
    Gm12878 Ctcf Chip Seq Data, supplied by Chrom Tech, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ctcf+chip-seq+data/chip+ctcf+data+gm12878+seq/pmc12715305-41-3-20
    Average 86 stars, based on 1 article reviews
    gm12878 ctcf chip seq data - by Bioz Stars, 2026-10
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    Images

    1) Product Images from "Chrom-Sig: de-noising 1D genomic profiles by signal processing methods"

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

    Journal: Bioinformatics

    doi: 10.1093/bioinformatics/btaf645

    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.
    Figure Legend 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.

    Techniques Used: ChIP-sequencing, Binding Assay, Generated

    Related Articles

    Chromatin Immunoprecipitation:

    Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods.
    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 (Figure 1a). ..

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

    Article Title: Chrom-Sig: de-noising 1D genomic profiles by signal processing methods
    Article Snippet: We verified with other GM12878 CTCF ChIP-seq and CUT&RUN data that Chrom-Sig was specific in identifying peaks overlapping known CTCF motifs ( , available as at Bioinformatics online). .. Similarly, Chrom-Sig particularly enriched for active promoters and enhancers in ATAC-seq and RNA Polymerase II ChIP-seq data—as expected and desired ( , available as at Bioinformatics online). .. Finally, we compared Chrom-Sig to AtacWorks.

    Binding Assay:

    Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods.
    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 (Figure 1a). ..

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

    Generated:

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



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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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    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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    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