dpnii buffer  (New England Biolabs)


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  • 99
    Name:
    DpnII
    Description:
    DpnII 5 000 units
    Catalog Number:
    r0543l
    Price:
    290
    Size:
    5 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs dpnii buffer
    DpnII
    DpnII 5 000 units
    https://www.bioz.com/result/dpnii buffer/product/New England Biolabs
    Average 99 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    dpnii buffer - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay"

    Article Title: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

    Journal: bioRxiv

    doi: 10.1101/2020.03.02.973396

    MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random DNA phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average DpnII read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.
    Figure Legend Snippet: MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random DNA phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average DpnII read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.

    Techniques Used: Binding Assay

    Multiplexed Integrated Accessibility Assay (MIAA) measures local DNA accessibility of synthesized oligonucleotide phrase libraries. A) 100nt phrases are integrated into stem cells at a designated genomic locus. Stem cells are split and half are differentiated into definitive endoderm cells. Retinoic acid receptor fused to hyper-activated deoxyadenosine methylase (DAM) enzyme results in methylation of phrases that open DNA. DNA is extracted and half is exposed to DpnII, which cleaves unmethylated sequences, while half is exposed to DpnI, which cleaves methylated sequences. Sequences are PCR amplified and sequenced. B) DpnI and DpnII read counts measured from a single definitive endoderm replicate show difference between designed opening and closing phrases. C) Proportion of DpnII read counts measured from a single definitive endoderm replicate gives estimate of MIAA openness. D) 100nt native sequences that were differentially opening as measured by DNase-seq are differentially opening as measured by MIAA and different from randomly shuffled control sequences (significance measured by paired t-test). E) Differential accessibility as measured by log change in normalized DNase-seq reads and MIAA methylation proportion shows correlation between native differential accessibility and MIAA accessibility. The correlation reported is the Pearson correlation coefficient (r).
    Figure Legend Snippet: Multiplexed Integrated Accessibility Assay (MIAA) measures local DNA accessibility of synthesized oligonucleotide phrase libraries. A) 100nt phrases are integrated into stem cells at a designated genomic locus. Stem cells are split and half are differentiated into definitive endoderm cells. Retinoic acid receptor fused to hyper-activated deoxyadenosine methylase (DAM) enzyme results in methylation of phrases that open DNA. DNA is extracted and half is exposed to DpnII, which cleaves unmethylated sequences, while half is exposed to DpnI, which cleaves methylated sequences. Sequences are PCR amplified and sequenced. B) DpnI and DpnII read counts measured from a single definitive endoderm replicate show difference between designed opening and closing phrases. C) Proportion of DpnII read counts measured from a single definitive endoderm replicate gives estimate of MIAA openness. D) 100nt native sequences that were differentially opening as measured by DNase-seq are differentially opening as measured by MIAA and different from randomly shuffled control sequences (significance measured by paired t-test). E) Differential accessibility as measured by log change in normalized DNase-seq reads and MIAA methylation proportion shows correlation between native differential accessibility and MIAA accessibility. The correlation reported is the Pearson correlation coefficient (r).

    Techniques Used: Synthesized, Methylation, Polymerase Chain Reaction, Amplification

    Related Articles

    Amplification:

    Article Title: A Scalable Gene Synthesis Platform Using High-Fidelity DNA Microchips
    Article Snippet: .. PCR amplification was followed by γ exonuclease digestion of 5′ phosphorylated strands, hybridization of the 3′ primer site to its complement, and cleavage of the 5′ and 3′ primer sites using USER enzyme mix and DpnII (New England Biolabs), respectively. .. Plate subpools were amplified from1 μL of OLS Pool 2 in 50 μL Phusion polymerase PCR reactions.

    Article Title: Chromatin state changes during neural development revealed by in vivo cell-type specific profiling
    Article Snippet: .. PCR adaptors were ligated to the cut DNA, before digestion with Dpn II (NEB) and PCR amplification (Clontech Advantage cDNA polymerase). .. Next-generation sequencing and data processing Following the DamID procedure, samples were sonicated in a Bioruptor Plus (Diagenode) to reduce the average DNA fragment size to 300 bp, and DamID adaptors were removed via either overnight Sau 3AI or Alw I digestion.

    Ligation:

    Article Title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination
    Article Snippet: .. DpnII or NlaIII was inactivated at 65°C for 20 min and samples were subjected to ligation under diluted condition with T4 DNA ligase (100 units, NEB, M0202L). ..

    Produced:

    Article Title: Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
    Article Snippet: .. 3C in maize The 3C sample was produced according to a previously described method [ ], and the DNA was digested with the enzyme DpnII (NEB, Category Number R0543). ..

    Polymerase Chain Reaction:

    Article Title: A Scalable Gene Synthesis Platform Using High-Fidelity DNA Microchips
    Article Snippet: .. PCR amplification was followed by γ exonuclease digestion of 5′ phosphorylated strands, hybridization of the 3′ primer site to its complement, and cleavage of the 5′ and 3′ primer sites using USER enzyme mix and DpnII (New England Biolabs), respectively. .. Plate subpools were amplified from1 μL of OLS Pool 2 in 50 μL Phusion polymerase PCR reactions.

    Article Title: Chromatin state changes during neural development revealed by in vivo cell-type specific profiling
    Article Snippet: .. PCR adaptors were ligated to the cut DNA, before digestion with Dpn II (NEB) and PCR amplification (Clontech Advantage cDNA polymerase). .. Next-generation sequencing and data processing Following the DamID procedure, samples were sonicated in a Bioruptor Plus (Diagenode) to reduce the average DNA fragment size to 300 bp, and DamID adaptors were removed via either overnight Sau 3AI or Alw I digestion.

    Methylated DNA Immunoprecipitation:

    Article Title: Retroviral Integration Mutagenesis in Mice and Comparative Analysis in Human AML Identify Reduced PTP4A3 Expression as a Prognostic Indicator
    Article Snippet: .. MeDIP Ten µg genomic DNA was digested overnight with 100 U of DpnII (New England Biolabs, Ipswich, MA, USA). .. Four µg digested DNA was denatured for 10′ at 95°C and incubated with either 2.5 µg anti-5-methylcytidine (BI-MECY-1000, Eurogentec, Liège, Belgium) or mouse pre-immune IgG (Sigma-Aldrich, Zwijndrecht, The Netherlands) in 500 µL IP-buffer (PBS with 0.05% Triton X-100) for 2 hrs at 4°C, followed by incubation with 30 µL of washed beads (M-280 sheep-anti-mouse IgG, Invitrogen, San Diego, CA, USA) for 2 hrs at 4°C.

    Hybridization:

    Article Title: A Scalable Gene Synthesis Platform Using High-Fidelity DNA Microchips
    Article Snippet: .. PCR amplification was followed by γ exonuclease digestion of 5′ phosphorylated strands, hybridization of the 3′ primer site to its complement, and cleavage of the 5′ and 3′ primer sites using USER enzyme mix and DpnII (New England Biolabs), respectively. .. Plate subpools were amplified from1 μL of OLS Pool 2 in 50 μL Phusion polymerase PCR reactions.

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  • 99
    New England Biolabs dpnii restriction enzyme incubation buffer
    Dpnii Restriction Enzyme Incubation Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii restriction enzyme incubation buffer/product/New England Biolabs
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    dpnii restriction enzyme incubation buffer - by Bioz Stars, 2020-07
    99/100 stars
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    90
    New England Biolabs dpnii buffer
    MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random <t>DNA</t> phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average <t>DpnII</t> read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.
    Dpnii Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii buffer/product/New England Biolabs
    Average 90 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    dpnii buffer - by Bioz Stars, 2020-07
    90/100 stars
      Buy from Supplier

    90
    New England Biolabs 1x dpnii buffer
    MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random <t>DNA</t> phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average <t>DpnII</t> read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.
    1x Dpnii Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/1x dpnii buffer/product/New England Biolabs
    Average 90 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    1x dpnii buffer - by Bioz Stars, 2020-07
    90/100 stars
      Buy from Supplier

    Image Search Results


    MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random DNA phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average DpnII read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.

    Journal: bioRxiv

    Article Title: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

    doi: 10.1101/2020.03.02.973396

    Figure Lengend Snippet: MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random DNA phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average DpnII read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.

    Article Snippet: DpnII digest:20 ug genomic DNA + 20 uL DpnII buffer (New England Biolabs) + 4 uL DpnII 9New England Biolabs) + up to 200 uL water.

    Techniques: Binding Assay

    Multiplexed Integrated Accessibility Assay (MIAA) measures local DNA accessibility of synthesized oligonucleotide phrase libraries. A) 100nt phrases are integrated into stem cells at a designated genomic locus. Stem cells are split and half are differentiated into definitive endoderm cells. Retinoic acid receptor fused to hyper-activated deoxyadenosine methylase (DAM) enzyme results in methylation of phrases that open DNA. DNA is extracted and half is exposed to DpnII, which cleaves unmethylated sequences, while half is exposed to DpnI, which cleaves methylated sequences. Sequences are PCR amplified and sequenced. B) DpnI and DpnII read counts measured from a single definitive endoderm replicate show difference between designed opening and closing phrases. C) Proportion of DpnII read counts measured from a single definitive endoderm replicate gives estimate of MIAA openness. D) 100nt native sequences that were differentially opening as measured by DNase-seq are differentially opening as measured by MIAA and different from randomly shuffled control sequences (significance measured by paired t-test). E) Differential accessibility as measured by log change in normalized DNase-seq reads and MIAA methylation proportion shows correlation between native differential accessibility and MIAA accessibility. The correlation reported is the Pearson correlation coefficient (r).

    Journal: bioRxiv

    Article Title: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

    doi: 10.1101/2020.03.02.973396

    Figure Lengend Snippet: Multiplexed Integrated Accessibility Assay (MIAA) measures local DNA accessibility of synthesized oligonucleotide phrase libraries. A) 100nt phrases are integrated into stem cells at a designated genomic locus. Stem cells are split and half are differentiated into definitive endoderm cells. Retinoic acid receptor fused to hyper-activated deoxyadenosine methylase (DAM) enzyme results in methylation of phrases that open DNA. DNA is extracted and half is exposed to DpnII, which cleaves unmethylated sequences, while half is exposed to DpnI, which cleaves methylated sequences. Sequences are PCR amplified and sequenced. B) DpnI and DpnII read counts measured from a single definitive endoderm replicate show difference between designed opening and closing phrases. C) Proportion of DpnII read counts measured from a single definitive endoderm replicate gives estimate of MIAA openness. D) 100nt native sequences that were differentially opening as measured by DNase-seq are differentially opening as measured by MIAA and different from randomly shuffled control sequences (significance measured by paired t-test). E) Differential accessibility as measured by log change in normalized DNase-seq reads and MIAA methylation proportion shows correlation between native differential accessibility and MIAA accessibility. The correlation reported is the Pearson correlation coefficient (r).

    Article Snippet: DpnII digest:20 ug genomic DNA + 20 uL DpnII buffer (New England Biolabs) + 4 uL DpnII 9New England Biolabs) + up to 200 uL water.

    Techniques: Synthesized, Methylation, Polymerase Chain Reaction, Amplification