dnasei Search Results


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  • 93
    GE Healthcare dnasei
    The early S-phase focal replication pattern does not result from differential access of <t>DNaseI.</t> Each column reflects a single cell stained for DAPI (upper panels), <t>BrdU</t> incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.
    Dnasei, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 93/100, based on 170 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TaKaRa with dnasei
    The early S-phase focal replication pattern does not result from differential access of <t>DNaseI.</t> Each column reflects a single cell stained for DAPI (upper panels), <t>BrdU</t> incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.
    With Dnasei, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen dnasei
    The early S-phase focal replication pattern does not result from differential access of <t>DNaseI.</t> Each column reflects a single cell stained for DAPI (upper panels), <t>BrdU</t> incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.
    Dnasei, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1503 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    MACHEREY NAGEL dnasei digestion
    The early S-phase focal replication pattern does not result from differential access of <t>DNaseI.</t> Each column reflects a single cell stained for DAPI (upper panels), <t>BrdU</t> incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.
    Dnasei Digestion, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 91/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche dnasei digestion
    Expression profiles of RAP-containing genes. (A) to (J) Transcript levels of 10 selected target genes ( MOT3 , CYC8 , CBK1 , SSL2 , PUF3 , TOP3 , TUP1 , BUD8 , MSI1 and SSM4 respectively). Yeast cells were grown to exponential phase, total <t>RNA</t> was extracted and <t>DNAseI</t> digested. Reverse transcription was performed, and expression levels were quantified by qRT-PCR using amplicons upstream and downstream of RAPs as indicated in the respective figures. Values were normalized to the first 5’ amplicon and represent means ° SD n ≤ 3; ***p
    Dnasei Digestion, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche on column dnasei
    <t>DNA</t> supercoiling around TSSs and regulatory elements. ( a ) Graph showing bTMP binding, indicative of DNA supercoiling, +/− 20 kb around transcription start sites (TSSs) in the presence or absence of bleomycin for active and inactive genes. ( b ) Profiles showing the changes in DNA supercoiling around TSSs after inhibiting RNA polymerases and topoisomerases. ( c ) Graph showing distribution of DNA supercoiling +/−5 kb of <t>DNaseI</t> sensitive sites before and after transcription inhibition. ( d ) Profile of DNA supercoiling +/− 10 kb around CTCF and p300-CBP binding sites. CTCF binding sites for RPE1 cells were obtained from the ENCODE project. p300-CBP binding sites are for A549 cells from the ENCODE project. ( e ) Graph showing topoisomerase binding +/− 20 kb around CTCF binding sites as determined by ChIP-microarray. T-tests were used to show the peak signal was significantly different to randomly generated background data, P
    On Column Dnasei, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega rq dnasei
    <t>DNA</t> supercoiling around TSSs and regulatory elements. ( a ) Graph showing bTMP binding, indicative of DNA supercoiling, +/− 20 kb around transcription start sites (TSSs) in the presence or absence of bleomycin for active and inactive genes. ( b ) Profiles showing the changes in DNA supercoiling around TSSs after inhibiting RNA polymerases and topoisomerases. ( c ) Graph showing distribution of DNA supercoiling +/−5 kb of <t>DNaseI</t> sensitive sites before and after transcription inhibition. ( d ) Profile of DNA supercoiling +/− 10 kb around CTCF and p300-CBP binding sites. CTCF binding sites for RPE1 cells were obtained from the ENCODE project. p300-CBP binding sites are for A549 cells from the ENCODE project. ( e ) Graph showing topoisomerase binding +/− 20 kb around CTCF binding sites as determined by ChIP-microarray. T-tests were used to show the peak signal was significantly different to randomly generated background data, P
    Rq Dnasei, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 72 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    TaKaRa dnasei kit
    <t>DNA</t> supercoiling around TSSs and regulatory elements. ( a ) Graph showing bTMP binding, indicative of DNA supercoiling, +/− 20 kb around transcription start sites (TSSs) in the presence or absence of bleomycin for active and inactive genes. ( b ) Profiles showing the changes in DNA supercoiling around TSSs after inhibiting RNA polymerases and topoisomerases. ( c ) Graph showing distribution of DNA supercoiling +/−5 kb of <t>DNaseI</t> sensitive sites before and after transcription inhibition. ( d ) Profile of DNA supercoiling +/− 10 kb around CTCF and p300-CBP binding sites. CTCF binding sites for RPE1 cells were obtained from the ENCODE project. p300-CBP binding sites are for A549 cells from the ENCODE project. ( e ) Graph showing topoisomerase binding +/− 20 kb around CTCF binding sites as determined by ChIP-microarray. T-tests were used to show the peak signal was significantly different to randomly generated background data, P
    Dnasei Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche dnasei enzyme
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Enzyme, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche collagenasea dnasei
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Collagenasea Dnasei, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Quanta Biosciences perfecta dnasei
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Perfecta Dnasei, supplied by Quanta Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche dnasei buffer
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Buffer, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega dnasei rqi
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Rqi, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Promega dnasei digestion
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Digestion, supplied by Promega, used in various techniques. Bioz Stars score: 91/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Boehringer Mannheim dnasei treated
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Treated, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 89/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega dnasei kit
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Kit, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche dnasei digestions
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Digestions, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher dnasei treated
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Treated, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 286 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche dnasei powder
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    Dnasei Powder, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    TaKaRa u dnasei
    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The <t>DNaseI</t> <t>footprinting</t> protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.
    U Dnasei, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    The early S-phase focal replication pattern does not result from differential access of DNaseI. Each column reflects a single cell stained for DAPI (upper panels), BrdU incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: The early S-phase focal replication pattern does not result from differential access of DNaseI. Each column reflects a single cell stained for DAPI (upper panels), BrdU incorporation (middle panels), or TUNEL (lower panels, Intergen) at the indicated DNaseI concentration. Cells were treated with DNaseI (Sigma) and stained with an anti-BrdU antibody (Becton Dickinson). After secondary antibody application, cells were processed for TUNEL staining.

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: Staining, BrdU Incorporation Assay, TUNEL Assay, Concentration Assay

    Images of different replication patterns during S-phase progression. Panels from left to right reflect the progression of replication patterns during S-phase progression. Sites of BrdU incorporation were detected by an anti-BrdU antibody containing DNaseI (green, Amersham) and overlaid on DAPI staining of the nucleus (blue). The pattern labeled intermediate likely reflects a transition phase between focal and distributed patterns. All processed images were recompiled from images on several sections throughout the nucleus and, thus, reflect the staining pattern of the entire nucleus compressed into a two-dimensional image. The intensity of individual foci in the focal pattern is stronger than in the distributed pattern, although this is not apparent as a result of the imaging process.

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: Images of different replication patterns during S-phase progression. Panels from left to right reflect the progression of replication patterns during S-phase progression. Sites of BrdU incorporation were detected by an anti-BrdU antibody containing DNaseI (green, Amersham) and overlaid on DAPI staining of the nucleus (blue). The pattern labeled intermediate likely reflects a transition phase between focal and distributed patterns. All processed images were recompiled from images on several sections throughout the nucleus and, thus, reflect the staining pattern of the entire nucleus compressed into a two-dimensional image. The intensity of individual foci in the focal pattern is stronger than in the distributed pattern, although this is not apparent as a result of the imaging process.

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: BrdU Incorporation Assay, Staining, Labeling, Imaging

    Synchronization in early S-phase by hydroxyurea or aphidicolin results in the focal replication pattern. ( A ) WI-38 cells were released from contact inhibition into media containing BrdU and either 1.5 mM hydroxyurea, 2 μg/mL aphidicolin, or no drug. Twenty-four hours after release, cells were fixed, and immunofluorescence was performed. BrdU was detected by an anti-BrdU antibody containing DNaseI (Amersham, green). When cells are arrested in early S-phase by either hydroxyurea or aphidicolin, incorporation of BrdU is found only in perinucleolar foci. In contrast, when cells are allowed to progress through S-phase in the absence of drug, BrdU is incorporated throughout the nucleus. ( B ) Quantitation of patterns, comparing cells treated either with hydroxyurea, aphidicolin, or no drug. ( C ) WI-38 cells were released from contact inhibition into media containing 1.5 mM hydroxyurea. Twenty-four hours after release, the cells were washed in PBS and were restimulated into S-phase by replacement with drug-free media. Cells were pulse-labeled with BrdU for 10 min at hourly intervals after release. At 1 h, a majority of cells continue to display focal replication patterns. By 3–4 h after release, significant distribution of replication sites has occurred.

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: Synchronization in early S-phase by hydroxyurea or aphidicolin results in the focal replication pattern. ( A ) WI-38 cells were released from contact inhibition into media containing BrdU and either 1.5 mM hydroxyurea, 2 μg/mL aphidicolin, or no drug. Twenty-four hours after release, cells were fixed, and immunofluorescence was performed. BrdU was detected by an anti-BrdU antibody containing DNaseI (Amersham, green). When cells are arrested in early S-phase by either hydroxyurea or aphidicolin, incorporation of BrdU is found only in perinucleolar foci. In contrast, when cells are allowed to progress through S-phase in the absence of drug, BrdU is incorporated throughout the nucleus. ( B ) Quantitation of patterns, comparing cells treated either with hydroxyurea, aphidicolin, or no drug. ( C ) WI-38 cells were released from contact inhibition into media containing 1.5 mM hydroxyurea. Twenty-four hours after release, the cells were washed in PBS and were restimulated into S-phase by replacement with drug-free media. Cells were pulse-labeled with BrdU for 10 min at hourly intervals after release. At 1 h, a majority of cells continue to display focal replication patterns. By 3–4 h after release, significant distribution of replication sites has occurred.

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: Inhibition, Immunofluorescence, Quantitation Assay, Labeling

    BrdU foci contain replication proteins and are associated with internal nuclear lamin A/C structures. ( A ) The localization of p150 (CAF-1; upper panels, green) and PCNA (lower panels, green) was determined during G 1 - and S-phase progression. At the G 1 -S boundary, both CAF-1 and PCNA foci increase in intensity. The mouse monoclonal antibody against p150 (MAB1) was kindly provided by B. Stillman. Similar results were seen with antibodies to the p60 subunit of CAF-1. PCNA was visualized with a rabbit polyclonal antibody (Santa Cruz). ( B ) Localization of BrdU was compared to that of p150 (red) in S-phase cells. DNaseI was used to expose BrdU. For this experiment, replication sites were detected using a rat anti-BrdU antibody (Harlan/Sera-Lab, green). ( C ) Early S-phase BrdU patterns were compared to that of UBF (upper panels, red), a nucleolar transcription factor, and nuclear lamins A/C (lower panels, red). The rabbit polyclonal anti-UBF antibody was kindly provided by L. Rothblum. Lamins A/C were visualized with a mouse monoclonal antibody (636, Santa Cruz). In all images, DNA is visualized by DAPI staining (blue).

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: BrdU foci contain replication proteins and are associated with internal nuclear lamin A/C structures. ( A ) The localization of p150 (CAF-1; upper panels, green) and PCNA (lower panels, green) was determined during G 1 - and S-phase progression. At the G 1 -S boundary, both CAF-1 and PCNA foci increase in intensity. The mouse monoclonal antibody against p150 (MAB1) was kindly provided by B. Stillman. Similar results were seen with antibodies to the p60 subunit of CAF-1. PCNA was visualized with a rabbit polyclonal antibody (Santa Cruz). ( B ) Localization of BrdU was compared to that of p150 (red) in S-phase cells. DNaseI was used to expose BrdU. For this experiment, replication sites were detected using a rat anti-BrdU antibody (Harlan/Sera-Lab, green). ( C ) Early S-phase BrdU patterns were compared to that of UBF (upper panels, red), a nucleolar transcription factor, and nuclear lamins A/C (lower panels, red). The rabbit polyclonal anti-UBF antibody was kindly provided by L. Rothblum. Lamins A/C were visualized with a mouse monoclonal antibody (636, Santa Cruz). In all images, DNA is visualized by DAPI staining (blue).

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: Staining

    HCl treatment is disruptive to nuclear structure. ( A ) Top panels compare sites of BrdU incorporation (Harlan/Sera-Lab, green) to localization p150 (CAF-1; red) with increasing acid concentration. No DNaseI is used in this experiment. At concentrations

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: HCl treatment is disruptive to nuclear structure. ( A ) Top panels compare sites of BrdU incorporation (Harlan/Sera-Lab, green) to localization p150 (CAF-1; red) with increasing acid concentration. No DNaseI is used in this experiment. At concentrations

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: BrdU Incorporation Assay, Concentration Assay

    Early S-phase replication appears focal using other methods to denature DNA. ( A ) Early S-phase BrdU incorporation sites (green) were compared using different methods to denature DNA. Using either heat exposure or base denaturation, early S-phase replication patterns appear focal. ( B ) Quantitation of replication patterns. Later in S-phase, denaturation by NaOH or heat yields a distributed pattern similar to that generated by DNaseI.

    Journal: Genes & Development

    Article Title: Nuclear organization of DNA replication in primary mammalian cells

    doi:

    Figure Lengend Snippet: Early S-phase replication appears focal using other methods to denature DNA. ( A ) Early S-phase BrdU incorporation sites (green) were compared using different methods to denature DNA. Using either heat exposure or base denaturation, early S-phase replication patterns appear focal. ( B ) Quantitation of replication patterns. Later in S-phase, denaturation by NaOH or heat yields a distributed pattern similar to that generated by DNaseI.

    Article Snippet: Indirect immunofluorescence was performed using primary antibodies against BrdU supplemented with 10 U/mL DNaseI (Amersham), followed by exposure to secondary antibodies (Vector).

    Techniques: BrdU Incorporation Assay, Quantitation Assay, Generated

    Expression profiles of RAP-containing genes. (A) to (J) Transcript levels of 10 selected target genes ( MOT3 , CYC8 , CBK1 , SSL2 , PUF3 , TOP3 , TUP1 , BUD8 , MSI1 and SSM4 respectively). Yeast cells were grown to exponential phase, total RNA was extracted and DNAseI digested. Reverse transcription was performed, and expression levels were quantified by qRT-PCR using amplicons upstream and downstream of RAPs as indicated in the respective figures. Values were normalized to the first 5’ amplicon and represent means ° SD n ≤ 3; ***p

    Journal: PLoS ONE

    Article Title: Nascent RNA signaling to yeast RNA Pol II during transcription elongation

    doi: 10.1371/journal.pone.0194438

    Figure Lengend Snippet: Expression profiles of RAP-containing genes. (A) to (J) Transcript levels of 10 selected target genes ( MOT3 , CYC8 , CBK1 , SSL2 , PUF3 , TOP3 , TUP1 , BUD8 , MSI1 and SSM4 respectively). Yeast cells were grown to exponential phase, total RNA was extracted and DNAseI digested. Reverse transcription was performed, and expression levels were quantified by qRT-PCR using amplicons upstream and downstream of RAPs as indicated in the respective figures. Values were normalized to the first 5’ amplicon and represent means ° SD n ≤ 3; ***p

    Article Snippet: Concentration of the RNA was determined using Nanodrop 2000 (ThermoScientific) and 20μg were used for DNAseI digestion (Roche).

    Techniques: Expressing, Quantitative RT-PCR, Amplification

    DNA supercoiling around TSSs and regulatory elements. ( a ) Graph showing bTMP binding, indicative of DNA supercoiling, +/− 20 kb around transcription start sites (TSSs) in the presence or absence of bleomycin for active and inactive genes. ( b ) Profiles showing the changes in DNA supercoiling around TSSs after inhibiting RNA polymerases and topoisomerases. ( c ) Graph showing distribution of DNA supercoiling +/−5 kb of DNaseI sensitive sites before and after transcription inhibition. ( d ) Profile of DNA supercoiling +/− 10 kb around CTCF and p300-CBP binding sites. CTCF binding sites for RPE1 cells were obtained from the ENCODE project. p300-CBP binding sites are for A549 cells from the ENCODE project. ( e ) Graph showing topoisomerase binding +/− 20 kb around CTCF binding sites as determined by ChIP-microarray. T-tests were used to show the peak signal was significantly different to randomly generated background data, P

    Journal: Nature structural & molecular biology

    Article Title: Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

    doi: 10.1038/nsmb.2509

    Figure Lengend Snippet: DNA supercoiling around TSSs and regulatory elements. ( a ) Graph showing bTMP binding, indicative of DNA supercoiling, +/− 20 kb around transcription start sites (TSSs) in the presence or absence of bleomycin for active and inactive genes. ( b ) Profiles showing the changes in DNA supercoiling around TSSs after inhibiting RNA polymerases and topoisomerases. ( c ) Graph showing distribution of DNA supercoiling +/−5 kb of DNaseI sensitive sites before and after transcription inhibition. ( d ) Profile of DNA supercoiling +/− 10 kb around CTCF and p300-CBP binding sites. CTCF binding sites for RPE1 cells were obtained from the ENCODE project. p300-CBP binding sites are for A549 cells from the ENCODE project. ( e ) Graph showing topoisomerase binding +/− 20 kb around CTCF binding sites as determined by ChIP-microarray. T-tests were used to show the peak signal was significantly different to randomly generated background data, P

    Article Snippet: Residual DNA was removed by on-column DNaseI (Roche) treatment.

    Techniques: Binding Assay, Inhibition, Chromatin Immunoprecipitation, Microarray, Generated

    Organization and boundaries of supercoiling domains. ( a ) Microarray data showing bTMP binding, indicative of DNA supercoiling, at HSA 11p15.4 spanning two topological domains 31 . Distribution of DNaseI sensitive sites and CTCF binding sites in RPE1 cells obtained from the ENCODE project. ( b ) Venn diagram showing the overlap between topological domain boundaries 31 and supercoiling (SC) boundaries across HSA 11. The overlap was determined by taking a +/− 20 kb window at each topological boundary and assessing whether this overlapped with a SC boundary (P

    Journal: Nature structural & molecular biology

    Article Title: Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

    doi: 10.1038/nsmb.2509

    Figure Lengend Snippet: Organization and boundaries of supercoiling domains. ( a ) Microarray data showing bTMP binding, indicative of DNA supercoiling, at HSA 11p15.4 spanning two topological domains 31 . Distribution of DNaseI sensitive sites and CTCF binding sites in RPE1 cells obtained from the ENCODE project. ( b ) Venn diagram showing the overlap between topological domain boundaries 31 and supercoiling (SC) boundaries across HSA 11. The overlap was determined by taking a +/− 20 kb window at each topological boundary and assessing whether this overlapped with a SC boundary (P

    Article Snippet: Residual DNA was removed by on-column DNaseI (Roche) treatment.

    Techniques: Microarray, Binding Assay

    RNA polymerase and topoisomerases define supercoiling domains. Diagrams showing the arrangement of supercoiling domains at HSA Xq13.1 ( a ) and HSA 11p15.1 ( b ) and microarray data showing the distribution of RNA transcripts and ChIP for topoisomerase (topo) I, topoisomerase IIα and IIβ binding across the genomic loci. Transcription is presented as log2 (array signal) whilst ChIP data is shown as log2 (bound/input). B. Scatter plot showing the relationship between transcription and DNA supercoiling in under-wound, over-wound and stable domains. ( c ) Boxplots showing GC content, transcription start site density, DNaseI site frequency, “open chromatin”, RNA transcription, RNA polymerase II binding, topoisomerase I and topoisomerase IIβ binding at “over-wound”, “under-wound” or “stable” supercoiling domains. Boxplots are as described in Fig. 3 and outliers are shown as black dots. Significance was assessed by t-test and asterisks correspond to the P-value (no *, P > 0.05; *, P

    Journal: Nature structural & molecular biology

    Article Title: Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

    doi: 10.1038/nsmb.2509

    Figure Lengend Snippet: RNA polymerase and topoisomerases define supercoiling domains. Diagrams showing the arrangement of supercoiling domains at HSA Xq13.1 ( a ) and HSA 11p15.1 ( b ) and microarray data showing the distribution of RNA transcripts and ChIP for topoisomerase (topo) I, topoisomerase IIα and IIβ binding across the genomic loci. Transcription is presented as log2 (array signal) whilst ChIP data is shown as log2 (bound/input). B. Scatter plot showing the relationship between transcription and DNA supercoiling in under-wound, over-wound and stable domains. ( c ) Boxplots showing GC content, transcription start site density, DNaseI site frequency, “open chromatin”, RNA transcription, RNA polymerase II binding, topoisomerase I and topoisomerase IIβ binding at “over-wound”, “under-wound” or “stable” supercoiling domains. Boxplots are as described in Fig. 3 and outliers are shown as black dots. Significance was assessed by t-test and asterisks correspond to the P-value (no *, P > 0.05; *, P

    Article Snippet: Residual DNA was removed by on-column DNaseI (Roche) treatment.

    Techniques: Microarray, Chromatin Immunoprecipitation, Binding Assay

    FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The DNaseI footprinting protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.

    Journal: Molecular microbiology

    Article Title: Cyclic di-GMP inhibits Vibrio cholerae motility by repressing induction of transcription and inducing extracellular polysaccharide production

    doi: 10.1111/mmi.12432

    Figure Lengend Snippet: FlrA binding to the flrBC promoter is inhibited by c-di-GMP (A) The flrBC promoter (10 nM) was incubated with no protein (lane 1) or 60 nM FlrA (lanes 2-10). 40 μM (+) and 80μM (++) of c-di-GMP, ATP, or GTP were added as indicated. (B) 22.2 nM of flrBC promoter DNA was incubated with FlrA buffer, 533.33 nM FlrA protein, or 44.4 μM c-di-GMP and 533.33 nM FlrA protein. The DNaseI footprinting protection site, boxed in black lines, corresponds to −76 to −54 on the flrBC promoter DNA.

    Article Snippet: To initiate the footprinting assay, 0.15U of DnaseI enzyme (Roche) was added.

    Techniques: Binding Assay, Incubation, Footprinting