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Millipore cpg dna fragments
Presence of DNase I hypersensitive sites within <t>CpG</t> islands 32 and 27 in the absence of <t>DNA</t> methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.
Cpg Dna Fragments, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas"

Article Title: DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

Journal: The Journal of Experimental Medicine

doi: 10.1084/jem.20100204

Presence of DNase I hypersensitive sites within CpG islands 32 and 27 in the absence of DNA methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.
Figure Legend Snippet: Presence of DNase I hypersensitive sites within CpG islands 32 and 27 in the absence of DNA methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.

Techniques Used: DNA Methylation Assay, End Labeling, Southern Blot, Marker, Staining

Cell type–specific DNA methylation status at BCL6 intronic region. (A) The diagram depicts the genomic organization of the human BCL6 locus. Indicated are the two transcription start sites (arrows), the four CpG islands (17, 32, 27, and 38), and the exons (black rectangles). Below the cartoon, the results of genomic bisulfite sequencing are presented. Each line of circles indicates an individual clone sequenced in the analysis after bisulfite treatment and PCR. Open circles indicate CpG sites at which no DNA methylation is detected. Blackened circles indicate CpG sites which are methylated. Data shown is representative of the results of three independent biological replicates. (B) MIRA-chip analysis of Raji (top) and H929 (bottom) across the 5′ end of the BCL6 locus. Each vertical line represents the mean normalized log 2 ratio of enriched/input probe signal from two replicate samples, corresponding to the genomic location on chromosome 3 at the BCL6 locus (UCSC genome browser HG18) as listed on the x axis. Blue and yellow colors represent methylated and unmethylated regions, respectively.
Figure Legend Snippet: Cell type–specific DNA methylation status at BCL6 intronic region. (A) The diagram depicts the genomic organization of the human BCL6 locus. Indicated are the two transcription start sites (arrows), the four CpG islands (17, 32, 27, and 38), and the exons (black rectangles). Below the cartoon, the results of genomic bisulfite sequencing are presented. Each line of circles indicates an individual clone sequenced in the analysis after bisulfite treatment and PCR. Open circles indicate CpG sites at which no DNA methylation is detected. Blackened circles indicate CpG sites which are methylated. Data shown is representative of the results of three independent biological replicates. (B) MIRA-chip analysis of Raji (top) and H929 (bottom) across the 5′ end of the BCL6 locus. Each vertical line represents the mean normalized log 2 ratio of enriched/input probe signal from two replicate samples, corresponding to the genomic location on chromosome 3 at the BCL6 locus (UCSC genome browser HG18) as listed on the x axis. Blue and yellow colors represent methylated and unmethylated regions, respectively.

Techniques Used: DNA Methylation Assay, Methylation Sequencing, Polymerase Chain Reaction, Methylation, Chromatin Immunoprecipitation

Related Articles

other:

Article Title: Production of antibodies with peptide-CpG-DNA-liposome complex without carriers
Article Snippet: Preparation of protein (or peptide) and CpG-DNA co-encapsulated in liposome complexes The liposomes CHEMS, Chol, DOPE, and DSPC were purchased from Sigma-Aldrich (St. Louis, MO, USA).

Stable Transfection:

Article Title: Protein Kinase D1: A New Component in Toll-Like Receptor 9 Signaling
Article Snippet: The resulting immune complexes were subjected to in vitro kinase assay using Syntide-2 (Sigma) as a PKD substrate, as previously described ( ). .. RAW264.7 cells stably expressing empty vector, FLAG-tagged PKD1, FLAG-tagged PKD2, or FLAG-tagged PKD3 were stimulated with medium or CpG-B DNA for 30 min. Each FLAG-tagged PKD family protein or endogenous protein in TLR9 signaling (TLR9, MyD88, IRAK1, IRAK4, TRAF6, or TRAF3) in the cell lysates was immunoprecipitated with EZview Red ANTI-FLAG M2 Affinity Gel (Sigma) or Abs specific for each individual protein. .. The presence of PKDs and proteins in the TLR9-signaling pathway in the resulting immunoprecipitates was detected by Western blot using Abs specific for FLAG (Sigma), TLR9 (Imgenex, San Diego, CA), IRAK1 (Millipore, Billerica, MA), IRAK4 (Abgent, San Diego, CA), MyD88 (Santa Cruz), TRAF6 (Santa Cruz), or TRAF3 (Santa Cruz).

Expressing:

Article Title: Protein Kinase D1: A New Component in Toll-Like Receptor 9 Signaling
Article Snippet: The resulting immune complexes were subjected to in vitro kinase assay using Syntide-2 (Sigma) as a PKD substrate, as previously described ( ). .. RAW264.7 cells stably expressing empty vector, FLAG-tagged PKD1, FLAG-tagged PKD2, or FLAG-tagged PKD3 were stimulated with medium or CpG-B DNA for 30 min. Each FLAG-tagged PKD family protein or endogenous protein in TLR9 signaling (TLR9, MyD88, IRAK1, IRAK4, TRAF6, or TRAF3) in the cell lysates was immunoprecipitated with EZview Red ANTI-FLAG M2 Affinity Gel (Sigma) or Abs specific for each individual protein. .. The presence of PKDs and proteins in the TLR9-signaling pathway in the resulting immunoprecipitates was detected by Western blot using Abs specific for FLAG (Sigma), TLR9 (Imgenex, San Diego, CA), IRAK1 (Millipore, Billerica, MA), IRAK4 (Abgent, San Diego, CA), MyD88 (Santa Cruz), TRAF6 (Santa Cruz), or TRAF3 (Santa Cruz).

Plasmid Preparation:

Article Title: Protein Kinase D1: A New Component in Toll-Like Receptor 9 Signaling
Article Snippet: The resulting immune complexes were subjected to in vitro kinase assay using Syntide-2 (Sigma) as a PKD substrate, as previously described ( ). .. RAW264.7 cells stably expressing empty vector, FLAG-tagged PKD1, FLAG-tagged PKD2, or FLAG-tagged PKD3 were stimulated with medium or CpG-B DNA for 30 min. Each FLAG-tagged PKD family protein or endogenous protein in TLR9 signaling (TLR9, MyD88, IRAK1, IRAK4, TRAF6, or TRAF3) in the cell lysates was immunoprecipitated with EZview Red ANTI-FLAG M2 Affinity Gel (Sigma) or Abs specific for each individual protein. .. The presence of PKDs and proteins in the TLR9-signaling pathway in the resulting immunoprecipitates was detected by Western blot using Abs specific for FLAG (Sigma), TLR9 (Imgenex, San Diego, CA), IRAK1 (Millipore, Billerica, MA), IRAK4 (Abgent, San Diego, CA), MyD88 (Santa Cruz), TRAF6 (Santa Cruz), or TRAF3 (Santa Cruz).

Immunoprecipitation:

Article Title: Protein Kinase D1: A New Component in Toll-Like Receptor 9 Signaling
Article Snippet: The resulting immune complexes were subjected to in vitro kinase assay using Syntide-2 (Sigma) as a PKD substrate, as previously described ( ). .. RAW264.7 cells stably expressing empty vector, FLAG-tagged PKD1, FLAG-tagged PKD2, or FLAG-tagged PKD3 were stimulated with medium or CpG-B DNA for 30 min. Each FLAG-tagged PKD family protein or endogenous protein in TLR9 signaling (TLR9, MyD88, IRAK1, IRAK4, TRAF6, or TRAF3) in the cell lysates was immunoprecipitated with EZview Red ANTI-FLAG M2 Affinity Gel (Sigma) or Abs specific for each individual protein. .. The presence of PKDs and proteins in the TLR9-signaling pathway in the resulting immunoprecipitates was detected by Western blot using Abs specific for FLAG (Sigma), TLR9 (Imgenex, San Diego, CA), IRAK1 (Millipore, Billerica, MA), IRAK4 (Abgent, San Diego, CA), MyD88 (Santa Cruz), TRAF6 (Santa Cruz), or TRAF3 (Santa Cruz).

Methylation:

Article Title: Seladin-1 expression is regulated by promoter methylation in adrenal cancer
Article Snippet: DNA from cell lines and tissue samples (500 ng) was submitted to bisulphite modification using EpiTect Bisulfite Kit (Qiagen, Milan, Italy) following manufacturer's protocol. .. For each treatment, CpG Genome Universal Methylated and Unmethylated DNA (Chemicon International Inc, USA) were used as positive and negative controls to confirm specificity of methylation specific PCR (MSP). .. After bisulphite treatment, DNA was immediately submitted to PCR analysis.

Article Title: Loss of mismatch repair signaling impairs the WNT–bone morphogenetic protein crosstalk and the colonic homeostasis
Article Snippet: Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ. .. DKK1 gene sequencing and CpG island methylation analysis Genomic DNA from CECs derived from four Msh2+/− and four Msh2−/− mice was isolated using the GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma). .. The DKK1 gene was amplified using primer sequences listed in and the Phusion High-Fidelity PCR Kit (Thermo Fisher Scientific).

Article Title: TFF1 Promotes EMT-Like Changes through an Auto-Induction Mechanism
Article Snippet: The row melting data were analyzed with LightCycler® 480 Gene Scanning Software, obtaining the difference melting curves. .. CpG Genome™ Universal Methylated DNA (Millipore) was used as 100%, while DNA from MCF-7 was used as 0% (for the TFF1 promoter methylation [ ]). .. The two standards were mixed to obtain 0%, 25%, 50%, 75%, 90%, and 100% TFF1 promoter methylation.

Polymerase Chain Reaction:

Article Title: Seladin-1 expression is regulated by promoter methylation in adrenal cancer
Article Snippet: DNA from cell lines and tissue samples (500 ng) was submitted to bisulphite modification using EpiTect Bisulfite Kit (Qiagen, Milan, Italy) following manufacturer's protocol. .. For each treatment, CpG Genome Universal Methylated and Unmethylated DNA (Chemicon International Inc, USA) were used as positive and negative controls to confirm specificity of methylation specific PCR (MSP). .. After bisulphite treatment, DNA was immediately submitted to PCR analysis.

Sequencing:

Article Title: Loss of mismatch repair signaling impairs the WNT–bone morphogenetic protein crosstalk and the colonic homeostasis
Article Snippet: Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ. .. DKK1 gene sequencing and CpG island methylation analysis Genomic DNA from CECs derived from four Msh2+/− and four Msh2−/− mice was isolated using the GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma). .. The DKK1 gene was amplified using primer sequences listed in and the Phusion High-Fidelity PCR Kit (Thermo Fisher Scientific).

Derivative Assay:

Article Title: Loss of mismatch repair signaling impairs the WNT–bone morphogenetic protein crosstalk and the colonic homeostasis
Article Snippet: Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ. .. DKK1 gene sequencing and CpG island methylation analysis Genomic DNA from CECs derived from four Msh2+/− and four Msh2−/− mice was isolated using the GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma). .. The DKK1 gene was amplified using primer sequences listed in and the Phusion High-Fidelity PCR Kit (Thermo Fisher Scientific).

Mouse Assay:

Article Title: Loss of mismatch repair signaling impairs the WNT–bone morphogenetic protein crosstalk and the colonic homeostasis
Article Snippet: Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ. .. DKK1 gene sequencing and CpG island methylation analysis Genomic DNA from CECs derived from four Msh2+/− and four Msh2−/− mice was isolated using the GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma). .. The DKK1 gene was amplified using primer sequences listed in and the Phusion High-Fidelity PCR Kit (Thermo Fisher Scientific).

Isolation:

Article Title: Loss of mismatch repair signaling impairs the WNT–bone morphogenetic protein crosstalk and the colonic homeostasis
Article Snippet: Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ. .. DKK1 gene sequencing and CpG island methylation analysis Genomic DNA from CECs derived from four Msh2+/− and four Msh2−/− mice was isolated using the GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma). .. The DKK1 gene was amplified using primer sequences listed in and the Phusion High-Fidelity PCR Kit (Thermo Fisher Scientific).

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    Millipore cpg dna fragments
    Presence of DNase I hypersensitive sites within <t>CpG</t> islands 32 and 27 in the absence of <t>DNA</t> methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.
    Cpg Dna Fragments, supplied by Millipore, 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/cpg dna fragments/product/Millipore
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    cpg dna fragments - by Bioz Stars, 2021-04
    93/100 stars
      Buy from Supplier

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    Presence of DNase I hypersensitive sites within CpG islands 32 and 27 in the absence of DNA methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.

    Journal: The Journal of Experimental Medicine

    Article Title: DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

    doi: 10.1084/jem.20100204

    Figure Lengend Snippet: Presence of DNase I hypersensitive sites within CpG islands 32 and 27 in the absence of DNA methylation. (A) The diagram depicts the approximate location of the genomic features of the BCL6 locus along with the restriction fragments and probes used for indirect end labeling. The approximate locations of the observed hypersensitive sites are indicated on the diagram. (B) The 5′ end of the BCL6 locus was analyzed by DNase I digestion using the reference restriction enzyme XbaI. Wedges indicate concentrations of DNase I. The locations of restriction sites and the probe used for the Southern blot are depicted in A. Arrows indicate the major DNase I hypersensitive sites and their locations are summarized in A. Marker positions were measured from ethidium-stained gel before transfer. Data shown is representative of results from at least three independent experiments.

    Article Snippet: Input and methylated CpG DNA fragments were amplified (WGA2; Sigma-Aldrich), labeled with Cy3 and Cy5 random monomers (TriLink Biotechnologies), respectively, and hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array (Roche).

    Techniques: DNA Methylation Assay, End Labeling, Southern Blot, Marker, Staining

    Cell type–specific DNA methylation status at BCL6 intronic region. (A) The diagram depicts the genomic organization of the human BCL6 locus. Indicated are the two transcription start sites (arrows), the four CpG islands (17, 32, 27, and 38), and the exons (black rectangles). Below the cartoon, the results of genomic bisulfite sequencing are presented. Each line of circles indicates an individual clone sequenced in the analysis after bisulfite treatment and PCR. Open circles indicate CpG sites at which no DNA methylation is detected. Blackened circles indicate CpG sites which are methylated. Data shown is representative of the results of three independent biological replicates. (B) MIRA-chip analysis of Raji (top) and H929 (bottom) across the 5′ end of the BCL6 locus. Each vertical line represents the mean normalized log 2 ratio of enriched/input probe signal from two replicate samples, corresponding to the genomic location on chromosome 3 at the BCL6 locus (UCSC genome browser HG18) as listed on the x axis. Blue and yellow colors represent methylated and unmethylated regions, respectively.

    Journal: The Journal of Experimental Medicine

    Article Title: DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

    doi: 10.1084/jem.20100204

    Figure Lengend Snippet: Cell type–specific DNA methylation status at BCL6 intronic region. (A) The diagram depicts the genomic organization of the human BCL6 locus. Indicated are the two transcription start sites (arrows), the four CpG islands (17, 32, 27, and 38), and the exons (black rectangles). Below the cartoon, the results of genomic bisulfite sequencing are presented. Each line of circles indicates an individual clone sequenced in the analysis after bisulfite treatment and PCR. Open circles indicate CpG sites at which no DNA methylation is detected. Blackened circles indicate CpG sites which are methylated. Data shown is representative of the results of three independent biological replicates. (B) MIRA-chip analysis of Raji (top) and H929 (bottom) across the 5′ end of the BCL6 locus. Each vertical line represents the mean normalized log 2 ratio of enriched/input probe signal from two replicate samples, corresponding to the genomic location on chromosome 3 at the BCL6 locus (UCSC genome browser HG18) as listed on the x axis. Blue and yellow colors represent methylated and unmethylated regions, respectively.

    Article Snippet: Input and methylated CpG DNA fragments were amplified (WGA2; Sigma-Aldrich), labeled with Cy3 and Cy5 random monomers (TriLink Biotechnologies), respectively, and hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array (Roche).

    Techniques: DNA Methylation Assay, Methylation Sequencing, Polymerase Chain Reaction, Methylation, Chromatin Immunoprecipitation