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    Active Motif chip exo kit
    <t>Sp2</t> localizes to composite TALE factor–Nf-y recognition motifs. Genomic binding sites of Sp2 in MEFs were determined by <t>ChIP-exo</t> sequencing. A , schematic representation of Sp2. The Sp-box ( yellow ), the glutamine-rich domains ( Q-rich , red ), the nuclear localization signal ( NLS , green ), the Btd-box ( blue ), and the zinc fingers ( ZF , black bars ) are indicated. B ). C , representative genome browser screenshots showing Sp2 ChIP-exo peaks and corresponding Sp2 ChIP-seq peaks at the Amd1 and Rplp0 promoters. D , sequence motifs enriched in Sp2-binding regions. Logos were obtained by running MEME-ChIP with 100-bp sequences of the top 600 Sp2 ChIP-exo peaks using default parameters. The numbers next to the logos indicate the occurrence of the motifs and the statistical significance ( E -value). E , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in D . Of note, the GC box motif ( M3 ) was not locally enriched. F , sequence motifs obtained by adjusting the MEME search to long motifs (20 to 30 bp widths). G , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in F . Of note, the GC box motif ( M3 ) was not locally enriched.
    Chip Exo Kit, supplied by Active Motif, used in various techniques. Bioz Stars score: 83/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    chip exo kit - by Bioz Stars, 2020-02
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    Sp2 localizes to composite TALE factor–Nf-y recognition motifs. Genomic binding sites of Sp2 in MEFs were determined by ChIP-exo sequencing. A , schematic representation of Sp2. The Sp-box ( yellow ), the glutamine-rich domains ( Q-rich , red ), the nuclear localization signal ( NLS , green ), the Btd-box ( blue ), and the zinc fingers ( ZF , black bars ) are indicated. B ). C , representative genome browser screenshots showing Sp2 ChIP-exo peaks and corresponding Sp2 ChIP-seq peaks at the Amd1 and Rplp0 promoters. D , sequence motifs enriched in Sp2-binding regions. Logos were obtained by running MEME-ChIP with 100-bp sequences of the top 600 Sp2 ChIP-exo peaks using default parameters. The numbers next to the logos indicate the occurrence of the motifs and the statistical significance ( E -value). E , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in D . Of note, the GC box motif ( M3 ) was not locally enriched. F , sequence motifs obtained by adjusting the MEME search to long motifs (20 to 30 bp widths). G , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in F . Of note, the GC box motif ( M3 ) was not locally enriched.

    Journal: The Journal of Biological Chemistry

    Article Title: Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites

    doi: 10.1074/jbc.RA118.005341

    Figure Lengend Snippet: Sp2 localizes to composite TALE factor–Nf-y recognition motifs. Genomic binding sites of Sp2 in MEFs were determined by ChIP-exo sequencing. A , schematic representation of Sp2. The Sp-box ( yellow ), the glutamine-rich domains ( Q-rich , red ), the nuclear localization signal ( NLS , green ), the Btd-box ( blue ), and the zinc fingers ( ZF , black bars ) are indicated. B ). C , representative genome browser screenshots showing Sp2 ChIP-exo peaks and corresponding Sp2 ChIP-seq peaks at the Amd1 and Rplp0 promoters. D , sequence motifs enriched in Sp2-binding regions. Logos were obtained by running MEME-ChIP with 100-bp sequences of the top 600 Sp2 ChIP-exo peaks using default parameters. The numbers next to the logos indicate the occurrence of the motifs and the statistical significance ( E -value). E , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in D . Of note, the GC box motif ( M3 ) was not locally enriched. F , sequence motifs obtained by adjusting the MEME search to long motifs (20 to 30 bp widths). G , local motif enrichment analysis (using CentriMo 4.12.0) of the M1 and M2 motifs shown in F . Of note, the GC box motif ( M3 ) was not locally enriched.

    Article Snippet: For Sp2 ChIP-exo analysis we used the ChIP-exo kit from Active Motif in accordance with the manufacturer's instructions.

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Sequencing, Zinc-Fingers

    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