dpnii Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs dpnii
    Identification of mVIS. Strategy outline for identification of regions flanking DNA methylated viral integration sites (mVIS) within murine leukemias. Genomic DNA was digested with <t>DpnII</t> (step 1), followed by methylated DNA immunoprecipitation <t>(MeDIP,</t> step 2). MeDIP enriched fragments were ligated (step 3) and amplified using primers within the LTR (step 4). These fragments were hybridized on a DNA promoter array (step 5). Hypergeometric Analysis of Tiling Arrays (HAT) was used to identify regions flanking mVIS (step 6).
    Dpnii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1383 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii/product/New England Biolabs
    Average 99 stars, based on 1383 article reviews
    Price from $9.99 to $1999.99
    dpnii - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    92
    Illumina Inc dpnii
    Identification of mVIS. Strategy outline for identification of regions flanking DNA methylated viral integration sites (mVIS) within murine leukemias. Genomic DNA was digested with <t>DpnII</t> (step 1), followed by methylated DNA immunoprecipitation <t>(MeDIP,</t> step 2). MeDIP enriched fragments were ligated (step 3) and amplified using primers within the LTR (step 4). These fragments were hybridized on a DNA promoter array (step 5). Hypergeometric Analysis of Tiling Arrays (HAT) was used to identify regions flanking mVIS (step 6).
    Dpnii, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii/product/Illumina Inc
    Average 92 stars, based on 17 article reviews
    Price from $9.99 to $1999.99
    dpnii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    dpnii  (Roche)
    92
    Roche dpnii
    <t>DNA</t> restriction analyses. A) i) Phi93 and Phi145 (DAM negative) cut with Dpn1 (cuts methylated GATC) and <t>DpnII</t> (cuts unmethylated GATC). ii) Phi145, Phi93 (MTase positive) and Phi15 (MTase negative) with HphI. B) i) Plasmid pPiM.93DAM cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC) under induced (I) and un-induced (NI) conditions. ii) Plasmid pPTPi (P), pPiM.145I cut with HphI under induced (I) and un-induced (NI) conditions. iii) Plasmid pPTPi (P), pPiM.145II cut with HphI under induced (I) and un-induced (NI) conditions.
    Dpnii, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii/product/Roche
    Average 92 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    dpnii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    99
    New England Biolabs nebuffer dpnii
    <t>DNA</t> restriction analyses. A) i) Phi93 and Phi145 (DAM negative) cut with Dpn1 (cuts methylated GATC) and <t>DpnII</t> (cuts unmethylated GATC). ii) Phi145, Phi93 (MTase positive) and Phi15 (MTase negative) with HphI. B) i) Plasmid pPiM.93DAM cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC) under induced (I) and un-induced (NI) conditions. ii) Plasmid pPTPi (P), pPiM.145I cut with HphI under induced (I) and un-induced (NI) conditions. iii) Plasmid pPTPi (P), pPiM.145II cut with HphI under induced (I) and un-induced (NI) conditions.
    Nebuffer Dpnii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebuffer dpnii/product/New England Biolabs
    Average 99 stars, based on 93 article reviews
    Price from $9.99 to $1999.99
    nebuffer dpnii - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    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 106 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 106 article reviews
    Price from $9.99 to $1999.99
    dpnii buffer - by Bioz Stars, 2020-07
    90/100 stars
      Buy from Supplier

    85
    Illumina Inc dpnii dge kit
    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 Dge Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii dge kit/product/Illumina Inc
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    dpnii dge kit - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

    85
    New England Biolabs dpnii enzyme
    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 Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii enzyme/product/New England Biolabs
    Average 85 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    dpnii enzyme - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

    95
    New England Biolabs dpnii reaction 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 Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii reaction buffer/product/New England Biolabs
    Average 95 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    dpnii reaction buffer - by Bioz Stars, 2020-07
    95/100 stars
      Buy from Supplier

    91
    MultiTherm dpnii
    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, supplied by MultiTherm, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpnii/product/MultiTherm
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dpnii - by Bioz Stars, 2020-07
    91/100 stars
      Buy from Supplier

    Image Search Results


    Identification of mVIS. Strategy outline for identification of regions flanking DNA methylated viral integration sites (mVIS) within murine leukemias. Genomic DNA was digested with DpnII (step 1), followed by methylated DNA immunoprecipitation (MeDIP, step 2). MeDIP enriched fragments were ligated (step 3) and amplified using primers within the LTR (step 4). These fragments were hybridized on a DNA promoter array (step 5). Hypergeometric Analysis of Tiling Arrays (HAT) was used to identify regions flanking mVIS (step 6).

    Journal: PLoS ONE

    Article Title: Retroviral Integration Mutagenesis in Mice and Comparative Analysis in Human AML Identify Reduced PTP4A3 Expression as a Prognostic Indicator

    doi: 10.1371/journal.pone.0026537

    Figure Lengend Snippet: Identification of mVIS. Strategy outline for identification of regions flanking DNA methylated viral integration sites (mVIS) within murine leukemias. Genomic DNA was digested with DpnII (step 1), followed by methylated DNA immunoprecipitation (MeDIP, step 2). MeDIP enriched fragments were ligated (step 3) and amplified using primers within the LTR (step 4). These fragments were hybridized on a DNA promoter array (step 5). Hypergeometric Analysis of Tiling Arrays (HAT) was used to identify regions flanking mVIS (step 6).

    Article Snippet: MeDIP Ten µg genomic DNA was digested overnight with 100 U of DpnII (New England Biolabs, Ipswich, MA, USA).

    Techniques: Methylation, Immunoprecipitation, Methylated DNA Immunoprecipitation, Amplification, HAT Assay

    Enrichment of 3T3-HOX11 DPs by cDNA RDA. (A) Ethidium-stained agarose gel electrophoresis of starting cDNA Dpn II fragment representations and various RDA enriched populations obtained by mutual subtraction of NIH 3T3 cells (3T3) with 3T3-HOX11 (left lanes show products obtained with NIH 3T3 cells as the tester and right lanes show products obtained with 3T3-HOX11 cells as the tester). Tester representation (R; unselected cDNA) and DP1, DP2, DP3, and DP4 are shown. The arrow indicates an enriched HOX11 Dpn II fragment identified by Southern filter hybridization with a HOX11 -specific probe. (B) Southern filter hybridizations (with Slim1 , Aldh1 , HOX11 , and β- actin probes as indicated) of the agarose gel-fractionated RDA DPs shown in panel A. Fragment sizes are indicated. (C) Northern filter hybridization of 10 μg of total RNA prepared from untransfected NIH 3T3 cells and three independent 3T3-HOX11 clones and hybridized with HOX11 , Slim1 , Aldh1 , and ATP synthase probes (as indicated). 3T3-HOX11 clones 5 and 18 were found to express HOX11 protein, while clone 11 did not (data not shown). Hybridization of the filter with ATP synthase was used to assess the quality of the RNA transferred.

    Journal: Molecular and Cellular Biology

    Article Title: The T-Cell Oncogenic Protein HOX11 Activates Aldh1 Expression in NIH 3T3 Cells but Represses Its Expression in Mouse Spleen Development

    doi:

    Figure Lengend Snippet: Enrichment of 3T3-HOX11 DPs by cDNA RDA. (A) Ethidium-stained agarose gel electrophoresis of starting cDNA Dpn II fragment representations and various RDA enriched populations obtained by mutual subtraction of NIH 3T3 cells (3T3) with 3T3-HOX11 (left lanes show products obtained with NIH 3T3 cells as the tester and right lanes show products obtained with 3T3-HOX11 cells as the tester). Tester representation (R; unselected cDNA) and DP1, DP2, DP3, and DP4 are shown. The arrow indicates an enriched HOX11 Dpn II fragment identified by Southern filter hybridization with a HOX11 -specific probe. (B) Southern filter hybridizations (with Slim1 , Aldh1 , HOX11 , and β- actin probes as indicated) of the agarose gel-fractionated RDA DPs shown in panel A. Fragment sizes are indicated. (C) Northern filter hybridization of 10 μg of total RNA prepared from untransfected NIH 3T3 cells and three independent 3T3-HOX11 clones and hybridized with HOX11 , Slim1 , Aldh1 , and ATP synthase probes (as indicated). 3T3-HOX11 clones 5 and 18 were found to express HOX11 protein, while clone 11 did not (data not shown). Hybridization of the filter with ATP synthase was used to assess the quality of the RNA transferred.

    Article Snippet: Double-stranded cDNA (approximately 2 μg) was digested with Dpn II (NEB), extracted with phenol-chloroform, and ethanol precipitated.

    Techniques: Staining, Agarose Gel Electrophoresis, Hybridization, Northern Blot, Clone Assay

    DNA restriction analyses. A) i) Phi93 and Phi145 (DAM negative) cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC). ii) Phi145, Phi93 (MTase positive) and Phi15 (MTase negative) with HphI. B) i) Plasmid pPiM.93DAM cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC) under induced (I) and un-induced (NI) conditions. ii) Plasmid pPTPi (P), pPiM.145I cut with HphI under induced (I) and un-induced (NI) conditions. iii) Plasmid pPTPi (P), pPiM.145II cut with HphI under induced (I) and un-induced (NI) conditions.

    Journal: BMC Genomics

    Article Title: Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity

    doi: 10.1186/1471-2164-15-831

    Figure Lengend Snippet: DNA restriction analyses. A) i) Phi93 and Phi145 (DAM negative) cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC). ii) Phi145, Phi93 (MTase positive) and Phi15 (MTase negative) with HphI. B) i) Plasmid pPiM.93DAM cut with Dpn1 (cuts methylated GATC) and DpnII (cuts unmethylated GATC) under induced (I) and un-induced (NI) conditions. ii) Plasmid pPTPi (P), pPiM.145I cut with HphI under induced (I) and un-induced (NI) conditions. iii) Plasmid pPTPi (P), pPiM.145II cut with HphI under induced (I) and un-induced (NI) conditions.

    Article Snippet: Restriction endonuclease digests were performed on phage DNA, plasmid DNA and bacterial genomic DNA using DpnI and DpnII (Roche, United States), or HphI (NEB, United States), all according to the manufacturer’s instructions.

    Techniques: Methylation, Plasmid Preparation

    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