nt cvipii  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 93

    Structured Review

    New England Biolabs nt cvipii
    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of <t>SDS</t> concentrations in <t>Nt.CviPII</t> activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Nt Cvipii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt cvipii/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nt cvipii - by Bioz Stars, 2022-05
    93/100 stars

    Images

    1) Product Images from "One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics"

    Article Title: One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-021-00427-2

    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Figure Legend Snippet: Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Techniques Used: Sonication, Activity Assay, Plasmid Preparation, Positive Control, Genome Wide, Sequencing

    2) Product Images from "NicE-seq: high resolution open chromatin profiling"

    Article Title: NicE-seq: high resolution open chromatin profiling

    Journal: Genome Biology

    doi: 10.1186/s13059-017-1247-6

    Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody
    Figure Legend Snippet: Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Techniques Used: Labeling, Agarose Gel Electrophoresis, Molecular Weight, Staining, Dot Blot

    3) Product Images from "One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics"

    Article Title: One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-021-00427-2

    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Figure Legend Snippet: Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Techniques Used: Sonication, Activity Assay, Plasmid Preparation, Positive Control, Genome Wide, Sequencing

    4) Product Images from "One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics"

    Article Title: One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-021-00427-2

    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Figure Legend Snippet: Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Techniques Used: Sonication, Activity Assay, Plasmid Preparation, Positive Control, Genome Wide, Sequencing

    5) Product Images from "One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics"

    Article Title: One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-021-00427-2

    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Figure Legend Snippet: Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Techniques Used: Sonication, Activity Assay, Plasmid Preparation, Positive Control, Genome Wide, Sequencing

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 93
    New England Biolabs nt cvipii
    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of <t>SDS</t> concentrations in <t>Nt.CviPII</t> activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom
    Nt Cvipii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt cvipii/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nt cvipii - by Bioz Stars, 2022-05
    93/100 stars
      Buy from Supplier

    Image Search Results


    Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Journal: Epigenetics & Chromatin

    Article Title: One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

    doi: 10.1186/s13072-021-00427-2

    Figure Lengend Snippet: Optimization of sonication free enzymatic condition for UniNicE-seq. A Effect of SDS concentrations in Nt.CviPII activity on plasmid DNA. Lane number 10 shows complete digestion of the plasmid DNA in the absence of SDS. B Effect of Triton X-100 in quenching of SDS mediated inhibitory activity of Nt.CviPII. Lane number 13 is the positive control. Triton X-100 concentrations were 1, 0.5, 0.125 and 0.1%, respectively. C Schematic representation of one-pot universal NicE-seq. D Comparison of FRiP scores of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. E Genome-wide comparison of accessible chromatin between one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells using sequence read density. F Peak annotation of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. G Genome-wide metagene plot of transcription start site (TSS) with ± 2 Kb of flanking region of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. H Genome-wide metagene plot of enhancer elements with ± 2 Kb of flanking region following enhancer start (ES) and enhancer end (EE) site of one-pot UniNicE-seq 500 cells and UniNicE-seq 25,000 cells. I Representative IGV genomic tracks of accessible chromatin of one-pot UniNicE-seq 500 cells compared with UniNicE-seq 25,000 cells. Gene names are indicated at the bottom

    Article Snippet: Different concentration of Triton was added along with SDS and the reaction was performed with Nt.CviPII as mentioned above.

    Techniques: Sonication, Activity Assay, Plasmid Preparation, Positive Control, Genome Wide, Sequencing

    Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Journal: Genome Biology

    Article Title: NicE-seq: high resolution open chromatin profiling

    doi: 10.1186/s13059-017-1247-6

    Figure Lengend Snippet: Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Article Snippet: Open chromatin DNA was labeled with biotin by incubating the nuclei in the presence of 2.5 U of Nt.CviPII (NEB R0626S), 10 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of biotin-14-dATP (Invitrogen, 19524-016) and 6 μM of biotin-16-dCTP (ChemCyte, CC-6003-1) in 200 μL of 1× NEB buffer 2.

    Techniques: Labeling, Agarose Gel Electrophoresis, Molecular Weight, Staining, Dot Blot