Structured Review

Illumina Inc mnase digested chromatin
Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with <t>MNase</t> and nuclease-protected DNA species sequenced using paired-end mode <t>Illumina</t> technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .
Mnase Digested Chromatin, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/mnase digested chromatin/product/Illumina Inc
Average 88 stars, based on 3 article reviews
Price from $9.99 to $1999.99
mnase digested chromatin - by Bioz Stars, 2020-09
88/100 stars

Images

1) Product Images from "SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae"

Article Title: SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1002974

Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .
Figure Legend Snippet: Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .

Techniques Used: Chromatin Immunoprecipitation, Sequencing, Mutagenesis

2) Product Images from "CLOCK:BMAL1 is a pioneer-like transcription factor"

Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor

Journal: Genes & Development

doi: 10.1101/gad.228536.113

CLOCK binds to DNA wrapped around nucleosomes. ( A ) CLOCK ChIP-seq signal on mononucleosome (i.e., mouse liver chromatin digested by MNase) at ZT22 (light blue; left ) and ZT06 (dark blue; right ) for the top 400 CLOCK:BMAL1 DNA-binding sites. The signal
Figure Legend Snippet: CLOCK binds to DNA wrapped around nucleosomes. ( A ) CLOCK ChIP-seq signal on mononucleosome (i.e., mouse liver chromatin digested by MNase) at ZT22 (light blue; left ) and ZT06 (dark blue; right ) for the top 400 CLOCK:BMAL1 DNA-binding sites. The signal

Techniques Used: Chromatin Immunoprecipitation, Binding Assay

Rhythmic CLOCK binding on DNA is associated with rhythmic H2A.Z signal at CLOCK:BMAL1 DNA-binding sites. ( A ) H2A.Z ChIP-seq over input signal ratio on MNase-treated chromatin in wild-type mice during the light phase (green) and dark phase (orange/red)
Figure Legend Snippet: Rhythmic CLOCK binding on DNA is associated with rhythmic H2A.Z signal at CLOCK:BMAL1 DNA-binding sites. ( A ) H2A.Z ChIP-seq over input signal ratio on MNase-treated chromatin in wild-type mice during the light phase (green) and dark phase (orange/red)

Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Mouse Assay

Related Articles

Sample Prep:

Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor
Article Snippet: .. Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome. ..

Mutagenesis:

Article Title: The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes *
Article Snippet: .. To examine nucleosomes across the genome in wild-type and mutant cells, we isolated mononucleosome DNA from MNase-digested chromatin for Illumina sequencing. .. Following sequence read alignments against the yeast reference genome (2003 Saccharomyces Genome Database genome build) in Bowtie, we determined the position and occupancy of nucleosomes using a template filtering algorithm ( ).

Isolation:

Article Title: The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes *
Article Snippet: .. To examine nucleosomes across the genome in wild-type and mutant cells, we isolated mononucleosome DNA from MNase-digested chromatin for Illumina sequencing. .. Following sequence read alignments against the yeast reference genome (2003 Saccharomyces Genome Database genome build) in Bowtie, we determined the position and occupancy of nucleosomes using a template filtering algorithm ( ).

Purification:

Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor
Article Snippet: .. Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome. ..

Article Title: Sperm is epigenetically programmed to regulate gene transcription in embryos
Article Snippet: .. For the generation of the input sample, 5%–10% of the MNase-digested chromatin was collected, and the same purification scheme was followed as with the immunoprecipitated chromatin prior to library preparation with a TruSeq DNA Kit (Illumina, #FC-121-2001). .. Sperm and spermatid chromatin were separated as described above, and 200 ng of digested genomic DNA were used to purify methylated DNA using the Methyl Collector TM Ultra Kit (Active Motif, #55005).

Immunoprecipitation:

Article Title: Sperm is epigenetically programmed to regulate gene transcription in embryos
Article Snippet: .. For the generation of the input sample, 5%–10% of the MNase-digested chromatin was collected, and the same purification scheme was followed as with the immunoprecipitated chromatin prior to library preparation with a TruSeq DNA Kit (Illumina, #FC-121-2001). .. Sperm and spermatid chromatin were separated as described above, and 200 ng of digested genomic DNA were used to purify methylated DNA using the Methyl Collector TM Ultra Kit (Active Motif, #55005).

Generated:

Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor
Article Snippet: .. Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome. ..

DNA Sequencing:

Article Title: SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae
Article Snippet: .. MNase digested chromatin samples processed for paired-end mode Illumina DNA sequencing. .. A. DNA from MNase digested chromatin fractions purified from wild-type and Δfun30 yeast strains separated by agarose gel electrophoresis and stained with ethidium bromide.

Sequencing:

Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor
Article Snippet: .. Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome. ..

Article Title: Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex
Article Snippet: .. MNase digested chromatin was reverse cross linked, and MNase sequencing libraries were prepared as previously described ( ) and sequenced using Illumina technology. .. Cell pellet was flash frozen in liquid nitrogen and kept in -80° C except for the spike-in experiment where both Sth1-degron and Kluyveromyces lactis cells were fixed in formaldehyde as described above, resuspended in water and cell concentration was determined under the microscope using a hemocytometer and 5% lactis were added to each sample.

Article Title: The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes *
Article Snippet: .. To examine nucleosomes across the genome in wild-type and mutant cells, we isolated mononucleosome DNA from MNase-digested chromatin for Illumina sequencing. .. Following sequence read alignments against the yeast reference genome (2003 Saccharomyces Genome Database genome build) in Bowtie, we determined the position and occupancy of nucleosomes using a template filtering algorithm ( ).

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    Illumina Inc mnase digested chromatin
    Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with <t>MNase</t> and nuclease-protected DNA species sequenced using paired-end mode <t>Illumina</t> technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .
    Mnase Digested Chromatin, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase digested chromatin/product/Illumina Inc
    Average 88 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    mnase digested chromatin - by Bioz Stars, 2020-09
    88/100 stars
      Buy from Supplier

    Image Search Results


    Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .

    Journal: PLoS Genetics

    Article Title: SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae

    doi: 10.1371/journal.pgen.1002974

    Figure Lengend Snippet: Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .

    Article Snippet: MNase digested chromatin samples processed for paired-end mode Illumina DNA sequencing.

    Techniques: Chromatin Immunoprecipitation, Sequencing, Mutagenesis

    CLOCK binds to DNA wrapped around nucleosomes. ( A ) CLOCK ChIP-seq signal on mononucleosome (i.e., mouse liver chromatin digested by MNase) at ZT22 (light blue; left ) and ZT06 (dark blue; right ) for the top 400 CLOCK:BMAL1 DNA-binding sites. The signal

    Journal: Genes & Development

    Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor

    doi: 10.1101/gad.228536.113

    Figure Lengend Snippet: CLOCK binds to DNA wrapped around nucleosomes. ( A ) CLOCK ChIP-seq signal on mononucleosome (i.e., mouse liver chromatin digested by MNase) at ZT22 (light blue; left ) and ZT06 (dark blue; right ) for the top 400 CLOCK:BMAL1 DNA-binding sites. The signal

    Article Snippet: Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome.

    Techniques: Chromatin Immunoprecipitation, Binding Assay

    Rhythmic CLOCK binding on DNA is associated with rhythmic H2A.Z signal at CLOCK:BMAL1 DNA-binding sites. ( A ) H2A.Z ChIP-seq over input signal ratio on MNase-treated chromatin in wild-type mice during the light phase (green) and dark phase (orange/red)

    Journal: Genes & Development

    Article Title: CLOCK:BMAL1 is a pioneer-like transcription factor

    doi: 10.1101/gad.228536.113

    Figure Lengend Snippet: Rhythmic CLOCK binding on DNA is associated with rhythmic H2A.Z signal at CLOCK:BMAL1 DNA-binding sites. ( A ) H2A.Z ChIP-seq over input signal ratio on MNase-treated chromatin in wild-type mice during the light phase (green) and dark phase (orange/red)

    Article Snippet: Sequencing libraries were generated using 50 ng of DNA purified from the MNase-digested chromatin (Illumina TruSeq DNA sample prep kit) and size-selected to ensure an insert size of a mononucleosome.

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Mouse Assay