epimark nucleosome assembly kit  (New England Biolabs)


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    Name:
    EpiMark Nucleosome Assembly Kit
    Description:
    EpiMark Nucleosome Assembly Kit 20 rxns
    Catalog Number:
    E5350S
    Price:
    598
    Size:
    20 rxns
    Category:
    DNA Methylases
    Score:
    85
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    Structured Review

    New England Biolabs epimark nucleosome assembly kit
    EpiMark Nucleosome Assembly Kit
    EpiMark Nucleosome Assembly Kit 20 rxns
    https://www.bioz.com/result/epimark nucleosome assembly kit/product/New England Biolabs
    Average 96 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    epimark nucleosome assembly kit - by Bioz Stars, 2019-11
    96/100 stars

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    Related Articles

    Methylation Sequencing:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: Assaying cytosine methylation from genomic DNA by bisulfite sequencing was performed as described ( ). .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Amplification:

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the reconstitution of recombinant nucleosomes used in activity assays, a 220 bp Widom 601 DNA sequence was first amplified by polymerase chain reaction (PCR) using unlabelled forward (gcgtaaGATATC ATCGATGGACCCTAT) and reverse (ttacgcGATATC ATCAGGTCGCTGTTC) primers (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Article Title: Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting
    Article Snippet: 5hmC- 5 μg of heterozygous placenta DNA was subject to DNA Glucosylation using the Epimark kit (New England Biolabs) and the DNA subject to digestion with 100 units of Msp 1 for a minimum of 8 hours at 37°C. .. The digested DNA was subject to ethanol precipitation and resuspended in a final volume of 20 μl TE.

    Mass Spectrometry:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: 4.3 Methylation-sensitive PCR (MS-PCR) was performed as described ( ). .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Electrophoresis:

    Article Title: Pin1 promotes histone H1 dephosphorylation and stabilizes its binding to chromatin
    Article Snippet: Nucleosomes were reconstituted using the EpiMark nucleosome assembly kit (New England Biolabs, Inc.) with some minor modifications ( ). .. One final dilution was performed in Tris, pH 7.5, 1 mM EDTA, 0.1% NP-40, 5 mM DTT, Complete protease inhibitors, 20% glycerol, and 100 µg/ml BSA to bring the final salt concentration to 0.1 M NaCl.

    Incubation:

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Activity Assay:

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the reconstitution of recombinant nucleosomes used in activity assays, a 220 bp Widom 601 DNA sequence was first amplified by polymerase chain reaction (PCR) using unlabelled forward (gcgtaaGATATC ATCGATGGACCCTAT) and reverse (ttacgcGATATC ATCAGGTCGCTGTTC) primers (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Article Title: Long non-coding RNA urothelial carcinoma associated 1 induces cell replication by inhibiting BRG1 in 5637 cells
    Article Snippet: Protein/DNA cross-links were reversed by adding 5 M NaCl and protein K at 65°C for 4 h. DNA was purified and amplified by PCR with primers for detecting human p21 promoter sequences: forward primer, 5′-GGAAATGTGTCCAGCGCACCAAC-3′ and reverse primer, 5′-CAGCGCGGCCCTGATATACAACC-3′. .. The measurements of the ATPase activity of BRG1 in the presence of nucleosome particles (using Nucleosome Assembly kit E5350S; NEB, Ipswich, MA, USA) was carried out as previously described ( ). .. Briefly, 100 ng of reconstituted nucleosomes were mixed with 1 μl of BRG1 and 1 μl Ci of [γ-32 P] ATP in a final volume of 10 μl (10 mM HEPES, pH 7.8, 50 mM KCl, 5 mM DTT, 0.5 mM PMSF, 200 g/ml BSA, 5% glycerol, 3.5 mM MgCl2 ).

    Expressing:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Briefly, HEK293T cells were transfected with in vitro methylated oct4TK-GFP reporter and/or effector expression plasmids. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Modification:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: HpaII resistance in % was determined from the ratio of HpaII digested versus control digested DNA and represents the fraction of modified cytosine residues (mC+hmC+fC+caC). .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Countercurrent Chromatography:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: DNA binding was performed using a 5′ biotinylated synthetic duplex 145 bp DNA (5′-CTT GCA TCG ATC CGA TTG AAC CAT CGC TCG GTG ACA GCT ACG TGA CTT AGT GTG CCC CAT CGA TCC AGT TCG ATC ACA GGC CAC CTG AGT CGA GAG TAT CGA CAC CCA GTG AAC GAT CGA TCC GAC TCG ATC GCC TCA CTG CTA G-3′) generated by scrambling the Widom-601 positioning sequence . .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Transfection:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA or genomic DNA (gnDNA) was recovered 48 h after transfection or at indicated time points using DNeasy Blood & Tissue kit (Qiagen). .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Generated:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: A Cy3-labeled DNA duplex was generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom-601 nucleosome positioning sequence . .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA by in vitro replication with unmethylated deoxynucleotides, such that approximately 95% of the resulting DNA molecules contain entirely unmethylated cytosines. .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: DNA binding was performed using a 5′ biotinylated synthetic duplex 145 bp DNA (5′-CTT GCA TCG ATC CGA TTG AAC CAT CGC TCG GTG ACA GCT ACG TGA CTT AGT GTG CCC CAT CGA TCC AGT TCG ATC ACA GGC CAC CTG AGT CGA GAG TAT CGA CAC CCA GTG AAC GAT CGA TCC GAC TCG ATC GCC TCA CTG CTA G-3′) generated by scrambling the Widom-601 positioning sequence . .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Article Title: Expansion of the ISWI chromatin remodeler family with new active complexes
    Article Snippet: For nucleosome reconstitution, DNA templates labeled at the 5′ position with Cy3 or Cy5 dyes were generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom‐601 nucleosome positioning sequence , or the Widom‐601 sequence flanked by 40 bp of arbitrary, non‐positioning sequence on each side. .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs), to produce homogeneous edge‐ or center‐positioned nucleosomes (see ).

    Imaging:

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol. .. Once reactions were complete, nucleosome assembly was determined by gel shift analysis.

    Sequencing:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: A Cy3-labeled DNA duplex was generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom-601 nucleosome positioning sequence . .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: Paragraph title: Sequencing experiments ... Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Monoucleosomes were prepared as previously described, with some slight changes. .. Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol. .. Briefly, 5 M NaCl was mixed with either unmethylated or methylated DNA (methylation of Widom 601 DNA described below) and dimer and tetramer histone proteins for each reaction.

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: Binding to nucleosome core particles was evaluated using commercially available purified human biotinylated mononucleosomes (EpiCypher). .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA. .. Biotinylated ligands were immobilized onto Streptavidin sensors (ForteBio) and steady-state binding was determined by dipping the sensor into the indicated concentrations of purified recombinant proteins.

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Article Title: Expansion of the ISWI chromatin remodeler family with new active complexes
    Article Snippet: For nucleosome reconstitution, DNA templates labeled at the 5′ position with Cy3 or Cy5 dyes were generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom‐601 nucleosome positioning sequence , or the Widom‐601 sequence flanked by 40 bp of arbitrary, non‐positioning sequence on each side. .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs), to produce homogeneous edge‐ or center‐positioned nucleosomes (see ).

    Sonication:

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: Naked genomic DNA purified from mouse macrophages was sonicated to obtain fragments ranging from 600 to 2000 bp. .. DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ).

    Binding Assay:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: Binding to nucleosome core particles was evaluated using commercially available purified human biotinylated mononucleosomes (EpiCypher). .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Article Title:
    Article Snippet: Nuc-1 was reconstituted in vitro using the EpiMarkTM Nucleosome Assembly kit (New England Biolabs) according to the dilution assembly protocol. .. The salt concentration was diluted to allow each histone tetramer to associate with two histone dimers and form the histone octamer on the DNA.

    ChIP-sequencing:

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ). .. In vitro assembled nucleosomes were digested with MNase and then incubated with macrophage-derived nuclear extracts to generate TF-nucleosome complexes.

    In Vivo:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: Assaying nucleosome positions in vivo by MNase sequencing was performed by modifiying an existing protocol ( ). .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    RNA Sequencing Assay:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: Total RNA was used to prepare strand-specific sequencing libraries with the Encore Complete RNA-Seq Library System I (NuGEN). .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Methylation:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA by in vitro replication with unmethylated deoxynucleotides, such that approximately 95% of the resulting DNA molecules contain entirely unmethylated cytosines. .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs). .. Assembled nucleosome positions were mapped by MNase sequencing, similar to the procedure for analyzing in vivo positions.

    Article Title: Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Ci
    Article Snippet: Paragraph title: Radioactive Methylation Assays ... Recombinant human core histones were purchased from New England Biolabs, and reconstituted nucleosomes were assembled using the EpiMark assembly kit (E5350S, New England Biolabs).

    Article Title: Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method
    Article Snippet: Paragraph title: Glucosylation of genomic DNA followed by methylation-sensitive qPCR (glucMS-qPCR) ... The ‘5hmC’ and ‘5hmC + 5mC’ levels in DHMRs containing Msp I/Hpa II sites were measured by a restriction enzyme-based assay (EpiMark kit, NEB) ( ).

    Article Title: Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting
    Article Snippet: Paragraph title: Methylation-sensitive genotyping ... 5hmC- 5 μg of heterozygous placenta DNA was subject to DNA Glucosylation using the Epimark kit (New England Biolabs) and the DNA subject to digestion with 100 units of Msp 1 for a minimum of 8 hours at 37°C.

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA was split into two parts and digested with either methylation-sensitive HpaII restriction enzyme or PvuII (unrelated control enzyme to fragment the genomic DNA) for 3 h. Via qPCR and the Roche Absolute quantification software tool we determined the arbitrary concentrations, taking into account the PCR-efficiency of each individual primer obtained by standard-curve measurements. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Flow Cytometry:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit). .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Labeling:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: Fluorescently labeled nucleosomes were used in nucleosome sliding assays. .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Expansion of the ISWI chromatin remodeler family with new active complexes
    Article Snippet: For nucleosome reconstitution, DNA templates labeled at the 5′ position with Cy3 or Cy5 dyes were generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom‐601 nucleosome positioning sequence , or the Widom‐601 sequence flanked by 40 bp of arbitrary, non‐positioning sequence on each side. .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs), to produce homogeneous edge‐ or center‐positioned nucleosomes (see ).

    Purification:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA by in vitro replication with unmethylated deoxynucleotides, such that approximately 95% of the resulting DNA molecules contain entirely unmethylated cytosines. .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs). .. Assembled nucleosome positions were mapped by MNase sequencing, similar to the procedure for analyzing in vivo positions.

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Monoucleosomes were prepared as previously described, with some slight changes. .. Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol. .. Briefly, 5 M NaCl was mixed with either unmethylated or methylated DNA (methylation of Widom 601 DNA described below) and dimer and tetramer histone proteins for each reaction.

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: Binding to nucleosome core particles was evaluated using commercially available purified human biotinylated mononucleosomes (EpiCypher). .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: Naked genomic DNA purified from mouse macrophages was sonicated to obtain fragments ranging from 600 to 2000 bp. .. DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ).

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ). .. Briefly, 8 μM of histone octamer was mixed with 25 pmol of either unlabelled or labelled Widom 601 DNA in a total volume of 100 μL.

    Article Title: BRD4 is a Histone Acetyltransferase that Evicts Nucleosomes from Chromatin
    Article Snippet: Purified 5S rDNA (208bp) was from New England Biolabs (NEB). .. Unmodified recombinant human nucleosomes were assembled on the 5S rDNA with purified human histone H2A/H2B dimers and histone H3/H4 tetramers using the EpiMark Nucleosome Assembly kit (NEB) following the manufacturer’s instructions. .. Cells were plated on cover slips and transfected with either a vector control or BRD4, with the addition of 5 mM sodium butyrate.

    Polymerase Chain Reaction:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: A Cy3-labeled DNA duplex was generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom-601 nucleosome positioning sequence . .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ). .. Briefly, 8 μM of histone octamer was mixed with 25 pmol of either unlabelled or labelled Widom 601 DNA in a total volume of 100 μL.

    Article Title: Expansion of the ISWI chromatin remodeler family with new active complexes
    Article Snippet: For nucleosome reconstitution, DNA templates labeled at the 5′ position with Cy3 or Cy5 dyes were generated by PCR and contained 80 bp of arbitrary sequence followed by the Widom‐601 nucleosome positioning sequence , or the Widom‐601 sequence flanked by 40 bp of arbitrary, non‐positioning sequence on each side. .. Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs), to produce homogeneous edge‐ or center‐positioned nucleosomes (see ).

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA was split into two parts and digested with either methylation-sensitive HpaII restriction enzyme or PvuII (unrelated control enzyme to fragment the genomic DNA) for 3 h. Via qPCR and the Roche Absolute quantification software tool we determined the arbitrary concentrations, taking into account the PCR-efficiency of each individual primer obtained by standard-curve measurements. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Filter-binding Assay:

    Article Title: Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Ci
    Article Snippet: Data of Km and k cat values were obtained with the filter binding assay by measuring the initial velocity of reaction at varied concentrations of one substrate and fixed saturating concentration of the other substrate, and fitting the kinetic data with a Michaelis-Menten equation. .. Recombinant human core histones were purchased from New England Biolabs, and reconstituted nucleosomes were assembled using the EpiMark assembly kit (E5350S, New England Biolabs).

    Electrophoretic Mobility Shift Assay:

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol. .. Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol.

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: DNA binding was performed using a 5′ biotinylated synthetic duplex 145 bp DNA (5′-CTT GCA TCG ATC CGA TTG AAC CAT CGC TCG GTG ACA GCT ACG TGA CTT AGT GTG CCC CAT CGA TCC AGT TCG ATC ACA GGC CAC CTG AGT CGA GAG TAT CGA CAC CCA GTG AAC GAT CGA TCC GAC TCG ATC GCC TCA CTG CTA G-3′) generated by scrambling the Widom-601 positioning sequence . .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Chromatin Immunoprecipitation:

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: Paragraph title: In vitro nucleosome assembly and in vitro ChIP ... DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ).

    Article Title:
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation (ChIP) Assay, Nuc Reconstitution, and Sequential ChIP ... Nuc-1 was reconstituted in vitro using the EpiMarkTM Nucleosome Assembly kit (New England Biolabs) according to the dilution assembly protocol.

    SDS Page:

    Article Title: Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Ci
    Article Snippet: For the gel-based assay, methylation mixtures were resolved on 16% SDS-PAGE, and the gel was dried and exposed to phosphor film for at least 36 h in the dark. .. Recombinant human core histones were purchased from New England Biolabs, and reconstituted nucleosomes were assembled using the EpiMark assembly kit (E5350S, New England Biolabs).

    Plasmid Preparation:

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA was split into two parts and digested with either methylation-sensitive HpaII restriction enzyme or PvuII (unrelated control enzyme to fragment the genomic DNA) for 3 h. Via qPCR and the Roche Absolute quantification software tool we determined the arbitrary concentrations, taking into account the PCR-efficiency of each individual primer obtained by standard-curve measurements. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Software:

    Article Title: Long non-coding RNA urothelial carcinoma associated 1 induces cell replication by inhibiting BRG1 in 5637 cells
    Article Snippet: The measurements of the ATPase activity of BRG1 in the presence of nucleosome particles (using Nucleosome Assembly kit E5350S; NEB, Ipswich, MA, USA) was carried out as previously described ( ). .. The measurements of the ATPase activity of BRG1 in the presence of nucleosome particles (using Nucleosome Assembly kit E5350S; NEB, Ipswich, MA, USA) was carried out as previously described ( ).

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA was split into two parts and digested with either methylation-sensitive HpaII restriction enzyme or PvuII (unrelated control enzyme to fragment the genomic DNA) for 3 h. Via qPCR and the Roche Absolute quantification software tool we determined the arbitrary concentrations, taking into account the PCR-efficiency of each individual primer obtained by standard-curve measurements. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Real-time Polymerase Chain Reaction:

    Article Title: Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method
    Article Snippet: Paragraph title: Glucosylation of genomic DNA followed by methylation-sensitive qPCR (glucMS-qPCR) ... The ‘5hmC’ and ‘5hmC + 5mC’ levels in DHMRs containing Msp I/Hpa II sites were measured by a restriction enzyme-based assay (EpiMark kit, NEB) ( ).

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Plasmid DNA was split into two parts and digested with either methylation-sensitive HpaII restriction enzyme or PvuII (unrelated control enzyme to fragment the genomic DNA) for 3 h. Via qPCR and the Roche Absolute quantification software tool we determined the arbitrary concentrations, taking into account the PCR-efficiency of each individual primer obtained by standard-curve measurements. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Recombinant:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA by in vitro replication with unmethylated deoxynucleotides, such that approximately 95% of the resulting DNA molecules contain entirely unmethylated cytosines. .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs). .. Assembled nucleosome positions were mapped by MNase sequencing, similar to the procedure for analyzing in vivo positions.

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: Naked genomic DNA purified from mouse macrophages was sonicated to obtain fragments ranging from 600 to 2000 bp. .. DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ). .. In vitro assembled nucleosomes were digested with MNase and then incubated with macrophage-derived nuclear extracts to generate TF-nucleosome complexes.

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the reconstitution of recombinant nucleosomes used in activity assays, a 220 bp Widom 601 DNA sequence was first amplified by polymerase chain reaction (PCR) using unlabelled forward (gcgtaaGATATC ATCGATGGACCCTAT) and reverse (ttacgcGATATC ATCAGGTCGCTGTTC) primers (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ).

    Article Title: BRD4 is a Histone Acetyltransferase that Evicts Nucleosomes from Chromatin
    Article Snippet: Purified 5S rDNA (208bp) was from New England Biolabs (NEB). .. Unmodified recombinant human nucleosomes were assembled on the 5S rDNA with purified human histone H2A/H2B dimers and histone H3/H4 tetramers using the EpiMark Nucleosome Assembly kit (NEB) following the manufacturer’s instructions. .. Cells were plated on cover slips and transfected with either a vector control or BRD4, with the addition of 5 mM sodium butyrate.

    Article Title: Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Ci
    Article Snippet: The methylation assays were also conducted for histone H4 protein and reconstituted nucleosomes to confirm the effect of H4 acetylation on its methylation by PRMT1 and PRMT5. .. Recombinant human core histones were purchased from New England Biolabs, and reconstituted nucleosomes were assembled using the EpiMark assembly kit (E5350S, New England Biolabs). .. The protein substrate was incubated with acetyl-CoA (20 μ m ) in the absence or presence of p300 or MOF (0.4 μ m ) in the reaction buffer (50 m m Hepes, pH 8.0, 50 m m NaCl, 1 m m EDTA, and 0.5 m m DTT) at 30 °C for 10 min. Then [14 C]AdoMet (15 μ m ) and PRMT1 (0.01 μ m ) or PRMT5 (0.1 μ m ) was added to the reaction mixture to initialize H4 methylation.

    In Vitro:

    Article Title: Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
    Article Snippet: For in vitro nucleosome position analyses, we first generated an unmethylated equivalent of O. lucimarinus genomic DNA by in vitro replication with unmethylated deoxynucleotides, such that approximately 95% of the resulting DNA molecules contain entirely unmethylated cytosines. .. Natively methylated O. lucimarinus genomic DNA or the unmethylated equivalent was assembled with purified recombinant histones into nucleosomes by salt dilution using an EpiMark Nucleosome Assembly Kit (New England Biolabs).

    Article Title: Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
    Article Snippet: Paragraph title: In vitro nucleosome assembly and in vitro ChIP ... DNA was combined with recombinant histones (EpiMark™ Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis ( ).

    Article Title: BRD4 is a Histone Acetyltransferase that Evicts Nucleosomes from Chromatin
    Article Snippet: Paragraph title: In vitro Nucleosome assembly ... Unmodified recombinant human nucleosomes were assembled on the 5S rDNA with purified human histone H2A/H2B dimers and histone H3/H4 tetramers using the EpiMark Nucleosome Assembly kit (NEB) following the manufacturer’s instructions.

    Article Title:
    Article Snippet: ChIP assays were conducted with reagents and Ab against SIRT1 (Santa Cruz sc-15404) and anti-SIRT6 from Abcam plc (Cambridge, UK) as previously reported ( ). .. Nuc-1 was reconstituted in vitro using the EpiMarkTM Nucleosome Assembly kit (New England Biolabs) according to the dilution assembly protocol. .. For this purpose, purified recombinant human histone H2A/H2B dimer and histone H3.1/H4 tetramer were mixed with a DNA substrate encoding Nuc-1 constructed by PCR with the primers used for the assay of chromatin accessibility of Nuc-1 of the il12a promoter.

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Briefly, HEK293T cells were transfected with in vitro methylated oct4TK-GFP reporter and/or effector expression plasmids. .. T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Ethanol Precipitation:

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ). .. Briefly, 8 μM of histone octamer was mixed with 25 pmol of either unlabelled or labelled Widom 601 DNA in a total volume of 100 μL.

    Article Title: Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting
    Article Snippet: 5hmC- 5 μg of heterozygous placenta DNA was subject to DNA Glucosylation using the Epimark kit (New England Biolabs) and the DNA subject to digestion with 100 units of Msp 1 for a minimum of 8 hours at 37°C. .. 5hmC- 5 μg of heterozygous placenta DNA was subject to DNA Glucosylation using the Epimark kit (New England Biolabs) and the DNA subject to digestion with 100 units of Msp 1 for a minimum of 8 hours at 37°C.

    DNA Methylation Assay:

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Paragraph title: Nucleosome Assembly and DNA Methylation ... Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol.

    Article Title: GADD45a physically and functionally interacts with TET1
    Article Snippet: Paragraph title: DNA methylation analysis and T4 β-glucosyltransferase (β-GT) treatment ... T4 β-glucosyltransferase (β-GT) treatment was performed according to manufacturer's instructions (NEB EpiMark Kit).

    Concentration Assay:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA. .. Binding measurements were carried out in 50 mM Tris pH 7.5, 1 mM TCEP, 0.5% BSA, 0.01% Tween-20, and 50 mM NaCl (peptide) or 150 mM NaCl (DNA and nucleosome).

    Article Title: A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes
    Article Snippet: For the synthesis of nucleosomes used in electrophoretic mobility shift assays, the same primers described above were used with the exception that the forward primer was synthesised with an IRDye®700 fluorophore attached at the 5′-end of the sequence (purchased from IDT). .. Following purification of both PCR products by ethanol precipitation and determination of the DNA concentration, nucleosome reconstitution was carried out as described in the EpiMark™ Nucleosome Assembly Kit (New England Biolabs; https://www.neb.com/protocols/2012/06/04/epimark-nucleosome-assembly-kit-e5350 ). .. Briefly, 8 μM of histone octamer was mixed with 25 pmol of either unlabelled or labelled Widom 601 DNA in a total volume of 100 μL.

    Article Title: Pin1 promotes histone H1 dephosphorylation and stabilizes its binding to chromatin
    Article Snippet: Nucleosomes were reconstituted using the EpiMark nucleosome assembly kit (New England Biolabs, Inc.) with some minor modifications ( ). .. Nucleosomes were reconstituted using the EpiMark nucleosome assembly kit (New England Biolabs, Inc.) with some minor modifications ( ).

    Article Title: Expansion of the ISWI chromatin remodeler family with new active complexes
    Article Snippet: Nucleosomes were reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs), to produce homogeneous edge‐ or center‐positioned nucleosomes (see ). .. Reaction mixtures contained 300 nM of ATPase alone or 60 nM of the indicated ISWI complex.

    Article Title: Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Ci
    Article Snippet: Data of Km and k cat values were obtained with the filter binding assay by measuring the initial velocity of reaction at varied concentrations of one substrate and fixed saturating concentration of the other substrate, and fitting the kinetic data with a Michaelis-Menten equation. .. Recombinant human core histones were purchased from New England Biolabs, and reconstituted nucleosomes were assembled using the EpiMark assembly kit (E5350S, New England Biolabs).

    Article Title:
    Article Snippet: Nuc-1 was reconstituted in vitro using the EpiMarkTM Nucleosome Assembly kit (New England Biolabs) according to the dilution assembly protocol. .. For this purpose, purified recombinant human histone H2A/H2B dimer and histone H3.1/H4 tetramer were mixed with a DNA substrate encoding Nuc-1 constructed by PCR with the primers used for the assay of chromatin accessibility of Nuc-1 of the il12a promoter.

    CTG Assay:

    Article Title: Non-canonical reader modules of BAZ1A promote recovery from DNA damage
    Article Snippet: DNA binding was performed using a 5′ biotinylated synthetic duplex 145 bp DNA (5′-CTT GCA TCG ATC CGA TTG AAC CAT CGC TCG GTG ACA GCT ACG TGA CTT AGT GTG CCC CAT CGA TCC AGT TCG ATC ACA GGC CAC CTG AGT CGA GAG TAT CGA CAC CCA GTG AAC GAT CGA TCC GAC TCG ATC GCC TCA CTG CTA G-3′) generated by scrambling the Widom-601 positioning sequence . .. Alternatively, similar results were obtained for samples reconstituted with the EpiMark Nucleosome Assembly Kit (New England Biolabs) from 5′ biotinylated synthetic Widom-601 positioning sequence, using the dilution assembly protocol under conditions that minimize any uncomplexed DNA.

    Staining:

    Article Title: Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability
    Article Snippet: Purified histones from the Epimark Nucleosome Assembly Kit (NEB E5350) and either 5s rDNA (NEB) or biotinylated Nucleosome Assembly 601 Sequence DNA (Widom 601) (Epicypher 18-0001) were combined following the dilution assembly protocol for 25 pmol. .. Once reactions were complete, nucleosome assembly was determined by gel shift analysis.

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    New England Biolabs epimark nucleosome assembly kit
    Epimark Nucleosome Assembly Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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