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    New England Biolabs micrococcal nuclease new england biolabs
    AGO2 knock-down affects nucleosome occupancy at TSSs bound by SWI/SNF. ( a ) HeLaS3 cells were transfected with a control siRNA (siCTRL) or a pool of AGO2 siRNA (siAGO2). Down-regulation of AGO2 protein was verified by western blot. GAPDH was used as loading control. ( b ) Chromatin from siCTRL- or siAGO2-treated HeLaS3 cells was digested by <t>MNase</t> and recovered <t>DNA</t> fragments were sequenced. Nucleosome occupancy profile for siCTRL and siAGO2 cells was plotted for TSSs with at least 30 swiRNAs (siCTRL, black line; siAGO2, green line). The occupancy at the nucleosome +1 (arrow) is reduced in AGO2 knock-down cells. ( c ) Bars height represents percent reduction of nucleosome occupancy (siAGO2 versus siCTRL) at TSS ±150 nt overlapped by at least the indicated number of swiRNAs (green), IgG-IP ‘other sRNAs’ (black) and AGO1-associated ‘other sRNAs’ (purple). ** P value
    Micrococcal Nuclease New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 207 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    New England Biolabs mnase
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    Mnase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1063 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    New England Biolabs 1x mnase buffer
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    1x Mnase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    New England Biolabs mnase i
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    Mnase I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 89/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    New England Biolabs mnase enzyme
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    Mnase Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    New England Biolabs micrococcal nucleases
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    Micrococcal Nucleases, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nucleases/product/New England Biolabs
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    90
    New England Biolabs mnase buffer
    BEN-2 shows B cell-specific <t>nucleosome</t> occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with <t>MNase</t> digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.
    Mnase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 222 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    AGO2 knock-down affects nucleosome occupancy at TSSs bound by SWI/SNF. ( a ) HeLaS3 cells were transfected with a control siRNA (siCTRL) or a pool of AGO2 siRNA (siAGO2). Down-regulation of AGO2 protein was verified by western blot. GAPDH was used as loading control. ( b ) Chromatin from siCTRL- or siAGO2-treated HeLaS3 cells was digested by MNase and recovered DNA fragments were sequenced. Nucleosome occupancy profile for siCTRL and siAGO2 cells was plotted for TSSs with at least 30 swiRNAs (siCTRL, black line; siAGO2, green line). The occupancy at the nucleosome +1 (arrow) is reduced in AGO2 knock-down cells. ( c ) Bars height represents percent reduction of nucleosome occupancy (siAGO2 versus siCTRL) at TSS ±150 nt overlapped by at least the indicated number of swiRNAs (green), IgG-IP ‘other sRNAs’ (black) and AGO1-associated ‘other sRNAs’ (purple). ** P value

    Journal: Nucleic Acids Research

    Article Title: ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites

    doi: 10.1093/nar/gku1387

    Figure Lengend Snippet: AGO2 knock-down affects nucleosome occupancy at TSSs bound by SWI/SNF. ( a ) HeLaS3 cells were transfected with a control siRNA (siCTRL) or a pool of AGO2 siRNA (siAGO2). Down-regulation of AGO2 protein was verified by western blot. GAPDH was used as loading control. ( b ) Chromatin from siCTRL- or siAGO2-treated HeLaS3 cells was digested by MNase and recovered DNA fragments were sequenced. Nucleosome occupancy profile for siCTRL and siAGO2 cells was plotted for TSSs with at least 30 swiRNAs (siCTRL, black line; siAGO2, green line). The occupancy at the nucleosome +1 (arrow) is reduced in AGO2 knock-down cells. ( c ) Bars height represents percent reduction of nucleosome occupancy (siAGO2 versus siCTRL) at TSS ±150 nt overlapped by at least the indicated number of swiRNAs (green), IgG-IP ‘other sRNAs’ (black) and AGO1-associated ‘other sRNAs’ (purple). ** P value

    Article Snippet: Isolation of nucleosomal DNA by micrococcal nuclease (MNase) digestion Digestion of chromatin from untreated, siCTRL- or siAGO2-treated HeLa S3 cells (2 × 106 ) was performed with 50 U of MNase (New England Biolabs) in 300 μl of permeabilization buffer (15 mM Tris–HCl pH 7.4, 300 mM sucrose, 60 mM KCl, 15 mM NaCl, 4 mM CaCl2 , 0.5 mM EGTA, 0.2% NP-40, 0.5 mM β-mercaptoethanol) for 20 min at 37°C.

    Techniques: Transfection, Western Blot

    BEN-2 shows B cell-specific nucleosome occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with MNase digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.

    Journal: bioRxiv

    Article Title: Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells

    doi: 10.1101/2020.02.16.941070

    Figure Lengend Snippet: BEN-2 shows B cell-specific nucleosome occupancy, chromatin accessibility and enrichment for the H3K27ac active enhancer histone mark across a panel of B cell lines. A. Nucleosome occupancy at BEN-2 as measured by ChART-PCR with MNase digestion. Data was normalised to the inaccessible SFTPA2 gene promoter such that a value of 1.0 represents fully compacted nucleosomes, and lower values indicate less compacted nucleosomes. B. Chromatin accessibility at BEN-2 as measured by ChART-PCR with DNase I digestion. Data have been normalised to the inaccessible SFTPA2 gene promoter. C. H3K27ac enrichment at BEN-2 as determined by ChIP-qPCR using the percent input method. Grey bars indicate H3K27ac enrichment at the target locus, and black bars show enrichment using a non-specific IgG control antibody. All data are presented as mean ± SEM from at least 3 biological replicates.

    Article Snippet: To assess nucleosome occupancy, 1000 Gel Units MNase (New England Biolabs) was used.

    Techniques: Polymerase Chain Reaction, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction