ctcf chip-exo Active Motif Search Results


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    Active Motif active motif chip exo kit
    Application of PAtCh-Cap to <t>CTCF</t> <t>ChIP-exo</t> data allowed for significant artifact removal and improved confidence in peak identification. ( A ) To identify high-confidence CTCF peaks, all peaks called with a 0.05 q -value threshold from the ChIP-exo data with (red) and without (black) input treatment were plotted as the –log(q-value) versus ranked peak number. High confidence peaks were determined to be those characterized by a –log( q -value) higher than the inflection point and a line with a slope of –tan 1 to the curve (denoted by vertical lines). ( B ) Venn diagram demonstrating the overlap of high-confidence peaks identified from data sets with and without input treatment (top). The number of CTCF motifs found within each pool is denoted and clearly shows that the percentage of CTCF containing peaks relative to the total increases substantially after input treatment. Venn diagrams for the overlap of blacklisted peaks with each of the above regions (bottom).
    Active Motif Chip Exo Kit, supplied by Active Motif, used in various techniques. Bioz Stars score: 90/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/active motif chip exo kit/product/Active Motif
    Average 90 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    active motif chip exo kit - by Bioz Stars, 2020-05
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    rad21  (Abcam)
    95
    Abcam rad21
    Application of PAtCh-Cap to <t>CTCF</t> <t>ChIP-exo</t> data allowed for significant artifact removal and improved confidence in peak identification. ( A ) To identify high-confidence CTCF peaks, all peaks called with a 0.05 q -value threshold from the ChIP-exo data with (red) and without (black) input treatment were plotted as the –log(q-value) versus ranked peak number. High confidence peaks were determined to be those characterized by a –log( q -value) higher than the inflection point and a line with a slope of –tan 1 to the curve (denoted by vertical lines). ( B ) Venn diagram demonstrating the overlap of high-confidence peaks identified from data sets with and without input treatment (top). The number of CTCF motifs found within each pool is denoted and clearly shows that the percentage of CTCF containing peaks relative to the total increases substantially after input treatment. Venn diagrams for the overlap of blacklisted peaks with each of the above regions (bottom).
    Rad21, supplied by Abcam, used in various techniques. Bioz Stars score: 95/100, based on 252 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rad21/product/Abcam
    Average 95 stars, based on 252 article reviews
    Price from $9.99 to $1999.99
    rad21 - by Bioz Stars, 2020-05
    95/100 stars
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    99
    Abcam h3k27ac
    Binding of Foxj1 at promoters is dependent on Rfx2 (A-B) Screenshot around the promoter of X . laevis rfx2 (A) or hdx (B) along with the sequence tags obtained in ChIPseq of H3K4me3, <t>H3K27ac,</t> Foxj1, or Rfx2 in wildtype and Foxj1 in Rfx2 morphants (MO). (C) Shown is a screenshot of the X . laevis genomic region containing the tubb2b gene with ChIPseq tracks as in (A). The position of all Rfx motifs is denoted in the bottom track. Foxj1 peaks that are reduced > 3-fold in the Rfx2 morphants compared to control are shaded. (D) Shown are sequencing tag histograms in peaks as labeled from ChIPseq of Foxj1 in wild-type progenitors or progenitors from Rfx2 morphants.
    H3k27ac, supplied by Abcam, used in various techniques. Bioz Stars score: 99/100, based on 2784 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k27ac/product/Abcam
    Average 99 stars, based on 2784 article reviews
    Price from $9.99 to $1999.99
    h3k27ac - by Bioz Stars, 2020-05
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    99
    Qiagen minelute pcr purification kit
    Binding of Foxj1 at promoters is dependent on Rfx2 (A-B) Screenshot around the promoter of X . laevis rfx2 (A) or hdx (B) along with the sequence tags obtained in ChIPseq of H3K4me3, <t>H3K27ac,</t> Foxj1, or Rfx2 in wildtype and Foxj1 in Rfx2 morphants (MO). (C) Shown is a screenshot of the X . laevis genomic region containing the tubb2b gene with ChIPseq tracks as in (A). The position of all Rfx motifs is denoted in the bottom track. Foxj1 peaks that are reduced > 3-fold in the Rfx2 morphants compared to control are shaded. (D) Shown are sequencing tag histograms in peaks as labeled from ChIPseq of Foxj1 in wild-type progenitors or progenitors from Rfx2 morphants.
    Minelute Pcr Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 16148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/minelute pcr purification kit/product/Qiagen
    Average 99 stars, based on 16148 article reviews
    Price from $9.99 to $1999.99
    minelute pcr purification kit - by Bioz Stars, 2020-05
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    Image Search Results


    Application of PAtCh-Cap to CTCF ChIP-exo data allowed for significant artifact removal and improved confidence in peak identification. ( A ) To identify high-confidence CTCF peaks, all peaks called with a 0.05 q -value threshold from the ChIP-exo data with (red) and without (black) input treatment were plotted as the –log(q-value) versus ranked peak number. High confidence peaks were determined to be those characterized by a –log( q -value) higher than the inflection point and a line with a slope of –tan 1 to the curve (denoted by vertical lines). ( B ) Venn diagram demonstrating the overlap of high-confidence peaks identified from data sets with and without input treatment (top). The number of CTCF motifs found within each pool is denoted and clearly shows that the percentage of CTCF containing peaks relative to the total increases substantially after input treatment. Venn diagrams for the overlap of blacklisted peaks with each of the above regions (bottom).

    Journal: Nucleic Acids Research

    Article Title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

    doi: 10.1093/nar/gkw741

    Figure Lengend Snippet: Application of PAtCh-Cap to CTCF ChIP-exo data allowed for significant artifact removal and improved confidence in peak identification. ( A ) To identify high-confidence CTCF peaks, all peaks called with a 0.05 q -value threshold from the ChIP-exo data with (red) and without (black) input treatment were plotted as the –log(q-value) versus ranked peak number. High confidence peaks were determined to be those characterized by a –log( q -value) higher than the inflection point and a line with a slope of –tan 1 to the curve (denoted by vertical lines). ( B ) Venn diagram demonstrating the overlap of high-confidence peaks identified from data sets with and without input treatment (top). The number of CTCF motifs found within each pool is denoted and clearly shows that the percentage of CTCF containing peaks relative to the total increases substantially after input treatment. Venn diagrams for the overlap of blacklisted peaks with each of the above regions (bottom).

    Article Snippet: Once covalently bound to the magnetic beads, the input samples were treated identically as described above for the CTCF ChIP-exo samples utilizing reagents and materials from the Active Motif ChIP-exo Kit.

    Techniques: Chromatin Immunoprecipitation

    Representative CTCF ChIP-exo read coverage tracks for the pericentromeric region of chromosome 1 ( A ) and the promoter of the KCNJ3 gene ( B ). The CTCF reads (blue) were normalized to the reads from the input control (green) using MACS2 ( 27 ) to generate the enrichment read coverage tracks (red). Peaks identified by the MACS2 peak caller (represented in the .bed tracks) are denoted as red or blue vertical lines for the CTCF ChIP-exo data sets with and without input treatment, respectively. Analysis of the genomic sequences underneath the remaining peaks after input treatment (vertical red lines) definitively showed that these sites contain the core CTCF motif as evidenced by alignment of the CTCF sequence logo beneath.

    Journal: Nucleic Acids Research

    Article Title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

    doi: 10.1093/nar/gkw741

    Figure Lengend Snippet: Representative CTCF ChIP-exo read coverage tracks for the pericentromeric region of chromosome 1 ( A ) and the promoter of the KCNJ3 gene ( B ). The CTCF reads (blue) were normalized to the reads from the input control (green) using MACS2 ( 27 ) to generate the enrichment read coverage tracks (red). Peaks identified by the MACS2 peak caller (represented in the .bed tracks) are denoted as red or blue vertical lines for the CTCF ChIP-exo data sets with and without input treatment, respectively. Analysis of the genomic sequences underneath the remaining peaks after input treatment (vertical red lines) definitively showed that these sites contain the core CTCF motif as evidenced by alignment of the CTCF sequence logo beneath.

    Article Snippet: Once covalently bound to the magnetic beads, the input samples were treated identically as described above for the CTCF ChIP-exo samples utilizing reagents and materials from the Active Motif ChIP-exo Kit.

    Techniques: Chromatin Immunoprecipitation, Genomic Sequencing, Sequencing

    From the input treated CTCF ChIP-exo data set, ( A ) read tag distributions around all genomic CTCF-bound sites shown in the four binned motif combinations (right panel) were centered on the midpoint of the CTCF consensus to generate a heat map (top left) which is summed below as an aggregate plot. Denoted in blue and red are the sense and antisense strand read enrichments around the core CTCF motif, respectively. The centralized CTCF core sequence and adjacent motifs are depicted above a color map representation of 50 bp DNA stretches containing the various motif combinations (right panel). ( B ) Heat maps from RNA-seq data depicting gene transcripts exhibiting a two-fold up- (green) or down-regulation (red) after CTCF depletion relative to the scrambled siRNA control (Scr). For each motif group, CTCF promoter occupation sites (defined as ±1000 bps around the transcription start site (TSS)) were intersected with the RNA-seq data and resulting altered gene sets were binned as individual heat maps. ( C ) Each gene set from ( B ) was subjected to Ingenuity Pathway Analysis (IPA, www.ingenuity.com ) to identify biological pathways uniquely modulated by each of the CTCF motif combinations. ( D–F ) The same analyses in ( A–C ) were performed separately on the core CTCF consensus with the newly identified 3′-CTCF motif.

    Journal: Nucleic Acids Research

    Article Title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

    doi: 10.1093/nar/gkw741

    Figure Lengend Snippet: From the input treated CTCF ChIP-exo data set, ( A ) read tag distributions around all genomic CTCF-bound sites shown in the four binned motif combinations (right panel) were centered on the midpoint of the CTCF consensus to generate a heat map (top left) which is summed below as an aggregate plot. Denoted in blue and red are the sense and antisense strand read enrichments around the core CTCF motif, respectively. The centralized CTCF core sequence and adjacent motifs are depicted above a color map representation of 50 bp DNA stretches containing the various motif combinations (right panel). ( B ) Heat maps from RNA-seq data depicting gene transcripts exhibiting a two-fold up- (green) or down-regulation (red) after CTCF depletion relative to the scrambled siRNA control (Scr). For each motif group, CTCF promoter occupation sites (defined as ±1000 bps around the transcription start site (TSS)) were intersected with the RNA-seq data and resulting altered gene sets were binned as individual heat maps. ( C ) Each gene set from ( B ) was subjected to Ingenuity Pathway Analysis (IPA, www.ingenuity.com ) to identify biological pathways uniquely modulated by each of the CTCF motif combinations. ( D–F ) The same analyses in ( A–C ) were performed separately on the core CTCF consensus with the newly identified 3′-CTCF motif.

    Article Snippet: Once covalently bound to the magnetic beads, the input samples were treated identically as described above for the CTCF ChIP-exo samples utilizing reagents and materials from the Active Motif ChIP-exo Kit.

    Techniques: Chromatin Immunoprecipitation, Sequencing, RNA Sequencing Assay, Indirect Immunoperoxidase Assay

    Binding of Foxj1 at promoters is dependent on Rfx2 (A-B) Screenshot around the promoter of X . laevis rfx2 (A) or hdx (B) along with the sequence tags obtained in ChIPseq of H3K4me3, H3K27ac, Foxj1, or Rfx2 in wildtype and Foxj1 in Rfx2 morphants (MO). (C) Shown is a screenshot of the X . laevis genomic region containing the tubb2b gene with ChIPseq tracks as in (A). The position of all Rfx motifs is denoted in the bottom track. Foxj1 peaks that are reduced > 3-fold in the Rfx2 morphants compared to control are shaded. (D) Shown are sequencing tag histograms in peaks as labeled from ChIPseq of Foxj1 in wild-type progenitors or progenitors from Rfx2 morphants.

    Journal: PLoS Genetics

    Article Title: Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression

    doi: 10.1371/journal.pgen.1006538

    Figure Lengend Snippet: Binding of Foxj1 at promoters is dependent on Rfx2 (A-B) Screenshot around the promoter of X . laevis rfx2 (A) or hdx (B) along with the sequence tags obtained in ChIPseq of H3K4me3, H3K27ac, Foxj1, or Rfx2 in wildtype and Foxj1 in Rfx2 morphants (MO). (C) Shown is a screenshot of the X . laevis genomic region containing the tubb2b gene with ChIPseq tracks as in (A). The position of all Rfx motifs is denoted in the bottom track. Foxj1 peaks that are reduced > 3-fold in the Rfx2 morphants compared to control are shaded. (D) Shown are sequencing tag histograms in peaks as labeled from ChIPseq of Foxj1 in wild-type progenitors or progenitors from Rfx2 morphants.

    Article Snippet: Native proteins were immunoprecipitated with antibodies directed against H3K4me3 (Active Motif, cat #39159; lot #01609004), H3K27ac (Abcam, cat #ab4729, lot #GR71158-2), or rad21 (Abcam, cat #ab992; commercially-available CTCF antibodies target regions not conserved in the X . laevis protein).

    Techniques: Binding Assay, Sequencing, Labeling