ne buffer  (New England Biolabs)


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    Structured Review

    New England Biolabs ne buffer
    Ne Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ne buffer/product/New England Biolabs
    Average 97 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    ne buffer - by Bioz Stars, 2022-09
    97/100 stars

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    New England Biolabs nuclear extraction ne buffer
    CUT RUN with <t>nuclear</t> <t>extraction</t> and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution <t>buffer</t> (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.
    Nuclear Extraction Ne Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nuclear extraction ne buffer/product/New England Biolabs
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nuclear extraction ne buffer - by Bioz Stars, 2022-09
    97/100 stars
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    90
    New England Biolabs eco ri
    CUT RUN with <t>nuclear</t> <t>extraction</t> and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution <t>buffer</t> (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.
    Eco Ri, supplied by New England Biolabs, 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/result/eco ri/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
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    eco ri - by Bioz Stars, 2022-09
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    88
    New England Biolabs ne buffer 2
    CUT RUN with <t>nuclear</t> <t>extraction</t> and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution <t>buffer</t> (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.
    Ne Buffer 2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ne buffer 2/product/New England Biolabs
    Average 88 stars, based on 1 article reviews
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    ne buffer 2 - by Bioz Stars, 2022-09
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    New England Biolabs nuclear extract ne buffer
    CUT RUN with <t>nuclear</t> <t>extraction</t> and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution <t>buffer</t> (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.
    Nuclear Extract Ne Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nuclear extract ne buffer/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nuclear extract ne buffer - by Bioz Stars, 2022-09
    95/100 stars
      Buy from Supplier

    Image Search Results


    CUT RUN with nuclear extraction and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution buffer (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.

    Journal: bioRxiv

    Article Title: A New CUT RUN Low Volume-Urea (LoV-U) protocol uncovers Wnt/β-catenin tissue-specific genomic targets

    doi: 10.1101/2022.07.06.498999

    Figure Lengend Snippet: CUT RUN with nuclear extraction and Urea-mediated release allows reproducible profiling of β-catenin binding in HEK293T. A. Genome coverage tracks of traditional CUT RUN (C R) for β-catenin and C R using urea in the elution buffer (C R-LoV-U: Low Volume-Urea, see Figure 2 for a complete explanation of the protocol) for β-catenin and IgG negative control, scaled to signal per million reads. Peak regions called by SEACR are shaded. C R-LoV-U shows enriched signal compared to traditional C R for β-catenin, and successfully recapitulates previously published ChIP-seq peaks at known WNT responsive elements, indicated by red lines corresponding to the exact positions of the β-catenin peaks called in Doumpas et al., 2019 . B. Genome coverage tracks of 3 biological replicates of the C R-LoV-U β-catenin and IgG negative control, showing reproducible signal enrichment across replicates. C. Left: Venn diagram of number of peaks called by SEACR for β-catenin replicates. The peaks called in 2 of 3 replicates were considered high-confidence and used for downstream analyses. Right: Pie chart showing genomic region annotations for β-catenin peaks. Bottom: Signal enrichment plot displaying fold-change over IgG control for each replicate over the high-confidence peak regions. D. Motif analysis results for high-confidence β-catenin peak regions, showing significant enrichment for TCF/LEF binding motifs. E. Gene Ontology analysis of the peak-associated genes, where the odds ratio (ratio of input list to reference list, x-axis) and the statistical significance (y-axis) for groups of “GO-biological processes” are represented, shows enrichment for several WNT pathway-related mechanisms.

    Article Snippet: Cells were washed three times in Nuclear Extraction (NE) buffer (HEPES-KOH pH-8.2 [20 mM], KCl [10 mM], Spermidine [0.5 mM], IGEPAL [0.05%], Glycerol [20%], Roche Complete Protease Inhibitor EDTA-Free), resuspended in 40 μl NE per sample and bound to 20 μl Magnetic ConA Agarose beads equilibrated in binding buffer.

    Techniques: Binding Assay, Negative Control, Chromatin Immunoprecipitation