λ exonuclease digestion Search Results


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  • 99
    New England Biolabs λ exonuclease digestion
    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the <t>λ</t> exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )
    λ Exonuclease Digestion, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease digestion/product/New England Biolabs
    Average 99 stars, based on 39 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease digestion - by Bioz Stars, 2020-08
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    95
    Thermo Fisher λ exonuclease fermentas digestion
    S1 nuclease protection mapping of the ABCA2 transcription start site. A 5′-end phosphorylated 479 bp double-stranded DNA template for the S1 probe was generated by PCR and digested with <t>λ</t> exonuclease to generate an antisense single-stranded DNA probe that was end labeled with [γ- 32 P]ATP and hybridized to total RNA from BE(2)-M17 neuroblastoma cells. Following digestion with S1 nuclease, the protected fragment was separated by electrophoresis in a 6% polyacrylamide–7 M urea gel followed by autoradiography. The antisense strand of the 479 bp DNA template was manually sequenced and the φX174 Hin f DNA ladder was radiolabeled with [γ- 32 P]ATP to serve as sequence and size markers respectively. An arrow indicates a major protected fragment of 152 bp, located 95 bp upstream of the ATG translation start site that represents the major transcription start site.
    λ Exonuclease Fermentas Digestion, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease fermentas digestion/product/Thermo Fisher
    Average 95 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease fermentas digestion - by Bioz Stars, 2020-08
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    88
    Boehringer Mannheim λ exonuclease digestion
    S1 nuclease protection mapping of the ABCA2 transcription start site. A 5′-end phosphorylated 479 bp double-stranded DNA template for the S1 probe was generated by PCR and digested with <t>λ</t> exonuclease to generate an antisense single-stranded DNA probe that was end labeled with [γ- 32 P]ATP and hybridized to total RNA from BE(2)-M17 neuroblastoma cells. Following digestion with S1 nuclease, the protected fragment was separated by electrophoresis in a 6% polyacrylamide–7 M urea gel followed by autoradiography. The antisense strand of the 479 bp DNA template was manually sequenced and the φX174 Hin f DNA ladder was radiolabeled with [γ- 32 P]ATP to serve as sequence and size markers respectively. An arrow indicates a major protected fragment of 152 bp, located 95 bp upstream of the ATG translation start site that represents the major transcription start site.
    λ Exonuclease Digestion, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease digestion/product/Boehringer Mannheim
    Average 88 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease digestion - by Bioz Stars, 2020-08
    88/100 stars
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    Image Search Results


    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the λ exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )

    Journal: Nature Communications

    Article Title: Simplified ChIP-exo assays

    doi: 10.1038/s41467-018-05265-7

    Figure Lengend Snippet: ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the λ exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )

    Article Snippet: The λ exonuclease digestion (100 µl) containing: 20 U λ exonuclease (NEB), 1 × λ exonuclease reaction buffer (NEB), 0.1% Triton-X 100, and 5% DMSO was incubated for 30 min at 37 °C; then washed with 10 mM Tris-HCl, pH 8.0 at 4 °C.

    Techniques: Chromatin Immunoprecipitation, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Produced

    High resolution detection of supercoiling states ( a ) Strategy for paired-end sequencing of TMP cross-linked DNA fragments. I. Illumina barcoded adapters are ligated to cross-linked fragments. II. The 5′ strand is digested with λ exonuclease. III. Using a primer complementary to the paired-end adapter, 10 rounds of primer extension were performed. IV. Ribo-Gs were added at the 3′ end using Terminal Transferase, V. A double stranded adapter with a 5′ CCC overhang was ligated. VI. One round of primer extension followed by cycles of library amplification were performed. Libraries were sequenced from the CCC overhang end. ( b ) TMP-seq was performed on control samples with two replicates. Reads were normalized for DNA sequence bias. The average normalized TMP-seq (y-axis Ave. sample/DNA) signal for every 10 bp in a 4 kb region surrounding the transcription start site (TSS) and transcription end site (TES) of all genes is plotted (top), and for expressed and silent genes separately (bottom). n.c. Normalized counts.

    Journal: Nature structural & molecular biology

    Article Title: Transcription-generated torsional stress destabilizes nucleosomes

    doi: 10.1038/nsmb.2723

    Figure Lengend Snippet: High resolution detection of supercoiling states ( a ) Strategy for paired-end sequencing of TMP cross-linked DNA fragments. I. Illumina barcoded adapters are ligated to cross-linked fragments. II. The 5′ strand is digested with λ exonuclease. III. Using a primer complementary to the paired-end adapter, 10 rounds of primer extension were performed. IV. Ribo-Gs were added at the 3′ end using Terminal Transferase, V. A double stranded adapter with a 5′ CCC overhang was ligated. VI. One round of primer extension followed by cycles of library amplification were performed. Libraries were sequenced from the CCC overhang end. ( b ) TMP-seq was performed on control samples with two replicates. Reads were normalized for DNA sequence bias. The average normalized TMP-seq (y-axis Ave. sample/DNA) signal for every 10 bp in a 4 kb region surrounding the transcription start site (TSS) and transcription end site (TES) of all genes is plotted (top), and for expressed and silent genes separately (bottom). n.c. Normalized counts.

    Article Snippet: After ligation of PE barcode adapters, the 5′ strand was digested using 25 U of λ exonuclease (NEB) for 30 minutes at 37°C.

    Techniques: Sequencing, Countercurrent Chromatography, Amplification

    S1 nuclease protection mapping of the ABCA2 transcription start site. A 5′-end phosphorylated 479 bp double-stranded DNA template for the S1 probe was generated by PCR and digested with λ exonuclease to generate an antisense single-stranded DNA probe that was end labeled with [γ- 32 P]ATP and hybridized to total RNA from BE(2)-M17 neuroblastoma cells. Following digestion with S1 nuclease, the protected fragment was separated by electrophoresis in a 6% polyacrylamide–7 M urea gel followed by autoradiography. The antisense strand of the 479 bp DNA template was manually sequenced and the φX174 Hin f DNA ladder was radiolabeled with [γ- 32 P]ATP to serve as sequence and size markers respectively. An arrow indicates a major protected fragment of 152 bp, located 95 bp upstream of the ATG translation start site that represents the major transcription start site.

    Journal: Nucleic Acids Research

    Article Title: Reciprocal regulation of expression of the human adenosine 5?-triphosphate binding cassette, sub-family A, transporter 2 (ABCA2) promoter by the early growth response-1 (EGR-1) and Sp-family transcription factors

    doi:

    Figure Lengend Snippet: S1 nuclease protection mapping of the ABCA2 transcription start site. A 5′-end phosphorylated 479 bp double-stranded DNA template for the S1 probe was generated by PCR and digested with λ exonuclease to generate an antisense single-stranded DNA probe that was end labeled with [γ- 32 P]ATP and hybridized to total RNA from BE(2)-M17 neuroblastoma cells. Following digestion with S1 nuclease, the protected fragment was separated by electrophoresis in a 6% polyacrylamide–7 M urea gel followed by autoradiography. The antisense strand of the 479 bp DNA template was manually sequenced and the φX174 Hin f DNA ladder was radiolabeled with [γ- 32 P]ATP to serve as sequence and size markers respectively. An arrow indicates a major protected fragment of 152 bp, located 95 bp upstream of the ATG translation start site that represents the major transcription start site.

    Article Snippet: Two micrograms of the PCR product was digested with λ exonuclease (Invitrogen) in 67 mM glycine–KOH pH 9.4, 2.5 mM MgCl2 , 50 µg/ml BSA at 37°C for 30 min to generate the antisense single-stranded DNA.

    Techniques: Generated, Polymerase Chain Reaction, Labeling, Electrophoresis, Autoradiography, Sequencing