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  • 94
    Zymo Research methylated dna ip kit
    Figure 5. <t>DNA</t> methylation events per chromosome after DNA enrichment with MethylAmp MeDIP <t>kit,</t> hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.
    Methylated Dna Ip Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 94/100, based on 200 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher high throughput methylated dna ip on chip promoter assays
    Figure 5. <t>DNA</t> methylation events per chromosome after DNA enrichment with MethylAmp MeDIP <t>kit,</t> hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.
    High Throughput Methylated Dna Ip On Chip Promoter Assays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abcam dna immunoprecipitation medip chip kit
    Figure 5. <t>DNA</t> methylation events per chromosome after DNA enrichment with MethylAmp MeDIP <t>kit,</t> hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.
    Dna Immunoprecipitation Medip Chip Kit, supplied by Abcam, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Active Motif methylation dna ip medip kit
    Targeting xCT induces histone and <t>DNA</t> methylation of the MUC1 promoter A. and B. MDA-MB-468 (A) or BT-20 (B) cells were treated with 1.0 mM or 1.5 mM SASP for 72 h, respectively. Soluble chromatin from control and SASP treated cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control region from the GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (untreated cells, assigned a value of 1). C. and D. Soluble chromatin from MDA-MB-468/CshRNA, MDA-MB-468/xCTshRNA (C), BT-20/CshRNA and BT-20/xCTshRNA (D) cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (CshRNA cells, assigned a value of 1). E. Genomic DNA from the indicated MDA-MB-468 (left) and BT-20 (right) cells was subjected to immunoprecipitation of methylated DNA <t>(MeDIP)</t> and the precipitates were analyzed by qPCR of the MUC1 gene promoter. The results (mean±SD of 3 determinations) are expressed as relative fold enrichment compared to that obtained from CshRNA expressing cells (assigned a value of 1).
    Methylation Dna Ip Medip Kit, supplied by Active Motif, used in various techniques. Bioz Stars score: 90/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cell Signaling Technology Inc simpledip methylated dna immunoprecipitation medip kit
    Targeting xCT induces histone and <t>DNA</t> methylation of the MUC1 promoter A. and B. MDA-MB-468 (A) or BT-20 (B) cells were treated with 1.0 mM or 1.5 mM SASP for 72 h, respectively. Soluble chromatin from control and SASP treated cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control region from the GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (untreated cells, assigned a value of 1). C. and D. Soluble chromatin from MDA-MB-468/CshRNA, MDA-MB-468/xCTshRNA (C), BT-20/CshRNA and BT-20/xCTshRNA (D) cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (CshRNA cells, assigned a value of 1). E. Genomic DNA from the indicated MDA-MB-468 (left) and BT-20 (right) cells was subjected to immunoprecipitation of methylated DNA <t>(MeDIP)</t> and the precipitates were analyzed by qPCR of the MUC1 gene promoter. The results (mean±SD of 3 determinations) are expressed as relative fold enrichment compared to that obtained from CshRNA expressing cells (assigned a value of 1).
    Simpledip Methylated Dna Immunoprecipitation Medip Kit, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies medip chip methylated dna immunoprecipitation
    Targeting xCT induces histone and <t>DNA</t> methylation of the MUC1 promoter A. and B. MDA-MB-468 (A) or BT-20 (B) cells were treated with 1.0 mM or 1.5 mM SASP for 72 h, respectively. Soluble chromatin from control and SASP treated cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control region from the GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (untreated cells, assigned a value of 1). C. and D. Soluble chromatin from MDA-MB-468/CshRNA, MDA-MB-468/xCTshRNA (C), BT-20/CshRNA and BT-20/xCTshRNA (D) cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (CshRNA cells, assigned a value of 1). E. Genomic DNA from the indicated MDA-MB-468 (left) and BT-20 (right) cells was subjected to immunoprecipitation of methylated DNA <t>(MeDIP)</t> and the precipitates were analyzed by qPCR of the MUC1 gene promoter. The results (mean±SD of 3 determinations) are expressed as relative fold enrichment compared to that obtained from CshRNA expressing cells (assigned a value of 1).
    Medip Chip Methylated Dna Immunoprecipitation, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abcam medip kits
    <t>DNA</t> methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) <t>MEDIP</t> with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P
    Medip Kits, supplied by Abcam, used in various techniques. Bioz Stars score: 94/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc 450k dna methylation chip
    <t>DNA</t> methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) <t>MEDIP</t> with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P
    450k Dna Methylation Chip, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna methylation chip preparation
    <t>DNA</t> methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) <t>MEDIP</t> with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P
    Dna Methylation Chip Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc infinium dna methylation chip
    <t>DNA</t> methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) <t>MEDIP</t> with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P
    Infinium Dna Methylation Chip, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kaneka Corp medip methylated dna immunoprecipitation medip
    <t>DNA</t> methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. <t>MeDIP</t> was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.
    Medip Methylated Dna Immunoprecipitation Medip, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna methylation chip data genome wide dna methylation
    <t>DNA</t> methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. <t>MeDIP</t> was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.
    Dna Methylation Chip Data Genome Wide Dna Methylation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Diagenode dna immunoprecipitation medip kit
    <t>DNA</t> methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. <t>MeDIP</t> was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.
    Dna Immunoprecipitation Medip Kit, supplied by Diagenode, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna immunoprecipitation medip
    <t>DNA</t> methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. <t>MeDIP</t> was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.
    Dna Immunoprecipitation Medip, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Active Motif dna medip
    Replicative efficiency of divergent mtDNA ES lines. CC9 mus , CC9 spretus , CC9 dunni and CC9 pahari ES cells were induced to differentiate into neural lineages over 21 days and were assessed at days 0 ( a ), 3 ( b ), 12 ( c ) and 21 ( d ) of differentiation for mtDNA copy number and ratios of 5mC and 5hmC. MtDNA copy number was assessed by real-time PCR. Levels of enrichment for 5mC and 5hmC were assessed by <t>MeDIP</t> using antibodies against 5mC and 5hmC, and real-time PCR across exon 2 of PolgA. The data are expressed as a ratio of mtDNA copy against 5mC/5hmC, where 5mC and 5hmC are indicative of <t>DNA</t> methylation and DNA demethylation, respectively. ** P
    Dna Medip, supplied by Active Motif, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Figure 5. DNA methylation events per chromosome after DNA enrichment with MethylAmp MeDIP kit, hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.

    Journal: Epigenetics

    Article Title: Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome

    doi: 10.4161/epi.7.1.18647

    Figure Lengend Snippet: Figure 5. DNA methylation events per chromosome after DNA enrichment with MethylAmp MeDIP kit, hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.

    Article Snippet: The aim of this study was to compare three commercial MeDIP protocols that can be used for high-throughput DNA enrichment: MagMeDIP KITTM (Diagenode), Methylated-DNA IP KIT (Zymo Research), and Methylamp™ Methylated DNA capture kit (Epigentek).

    Techniques: DNA Methylation Assay, Methylated DNA Immunoprecipitation, Hybridization

    Figure 4. DNA methylation events per chromosome after DNA enrichment with MagMeDIP kit, hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.

    Journal: Epigenetics

    Article Title: Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome

    doi: 10.4161/epi.7.1.18647

    Figure Lengend Snippet: Figure 4. DNA methylation events per chromosome after DNA enrichment with MagMeDIP kit, hybridization to Nimblegen 385K Human Promoter plus CpG Islands arrays and bioinformatics analysis.

    Article Snippet: The aim of this study was to compare three commercial MeDIP protocols that can be used for high-throughput DNA enrichment: MagMeDIP KITTM (Diagenode), Methylated-DNA IP KIT (Zymo Research), and Methylamp™ Methylated DNA capture kit (Epigentek).

    Techniques: DNA Methylation Assay, Hybridization

    Heterochromatin spreading is restricted to some retrotransposon families. The 144 families of class I retrotransposons represented by at least 1000 probes within the adjacent 4 kb were identified and the average level of H3K9me2, 5-methylcytosine and K3K27me3 enrichment was determined for 200 bp bins. The average values are calculated from both sides of annotated elements collapsed. (A) The relative level of DNA methylation in each 200 bp bin is shown for each of the 144 families. The red color indicates enrichment for the modification while blue indicates depletion of the mark. Black indicates levels of the modification similar to genome-wide average values. The color intensity is based on the average log ratio of immunoprecipitated DNA relative to input DNA. The retrotransposons are grouped according to whether they show spreading for DNA methylation and H3K9me2, H3K9me2 only or neither of the marks. Similar plots are shown for H3K9me2 (B) and H3K27me3 (C). (D) Whole-genome bisulphite sequencing data was used to assess the methylation level in different cytosine contexts in the low-copy (based on the absence of repetitive sequences) 1 kilobase regions flanking spreading (both), spreading (H3K9), non-spreading retrotransposons and for 10,000 random genomic regions. The error bars indicate standard deviation among retrotransposon families and “*” indicate significant (p

    Journal: PLoS Genetics

    Article Title: Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

    doi: 10.1371/journal.pgen.1003127

    Figure Lengend Snippet: Heterochromatin spreading is restricted to some retrotransposon families. The 144 families of class I retrotransposons represented by at least 1000 probes within the adjacent 4 kb were identified and the average level of H3K9me2, 5-methylcytosine and K3K27me3 enrichment was determined for 200 bp bins. The average values are calculated from both sides of annotated elements collapsed. (A) The relative level of DNA methylation in each 200 bp bin is shown for each of the 144 families. The red color indicates enrichment for the modification while blue indicates depletion of the mark. Black indicates levels of the modification similar to genome-wide average values. The color intensity is based on the average log ratio of immunoprecipitated DNA relative to input DNA. The retrotransposons are grouped according to whether they show spreading for DNA methylation and H3K9me2, H3K9me2 only or neither of the marks. Similar plots are shown for H3K9me2 (B) and H3K27me3 (C). (D) Whole-genome bisulphite sequencing data was used to assess the methylation level in different cytosine contexts in the low-copy (based on the absence of repetitive sequences) 1 kilobase regions flanking spreading (both), spreading (H3K9), non-spreading retrotransposons and for 10,000 random genomic regions. The error bars indicate standard deviation among retrotransposon families and “*” indicate significant (p

    Article Snippet: Briefly, methylated DNA was immunoprecipitated with an anti-5-methylcytosine monoclonal antibody from 400 ng sonicated DNA using the Methylated DNA IP Kit (Zymo Research, Orange, CA; Cat # D5101).

    Techniques: DNA Methylation Assay, Modification, Genome Wide, Immunoprecipitation, Bisulfite Sequencing, Methylation, Standard Deviation

    Targeting xCT induces histone and DNA methylation of the MUC1 promoter A. and B. MDA-MB-468 (A) or BT-20 (B) cells were treated with 1.0 mM or 1.5 mM SASP for 72 h, respectively. Soluble chromatin from control and SASP treated cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control region from the GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (untreated cells, assigned a value of 1). C. and D. Soluble chromatin from MDA-MB-468/CshRNA, MDA-MB-468/xCTshRNA (C), BT-20/CshRNA and BT-20/xCTshRNA (D) cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (CshRNA cells, assigned a value of 1). E. Genomic DNA from the indicated MDA-MB-468 (left) and BT-20 (right) cells was subjected to immunoprecipitation of methylated DNA (MeDIP) and the precipitates were analyzed by qPCR of the MUC1 gene promoter. The results (mean±SD of 3 determinations) are expressed as relative fold enrichment compared to that obtained from CshRNA expressing cells (assigned a value of 1).

    Journal: Oncotarget

    Article Title: Functional interactions of the cystine/glutamate antiporter, CD44v and MUC1-C oncoprotein in triple-negative breast cancer cells

    doi: 10.18632/oncotarget.7598

    Figure Lengend Snippet: Targeting xCT induces histone and DNA methylation of the MUC1 promoter A. and B. MDA-MB-468 (A) or BT-20 (B) cells were treated with 1.0 mM or 1.5 mM SASP for 72 h, respectively. Soluble chromatin from control and SASP treated cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control region from the GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (untreated cells, assigned a value of 1). C. and D. Soluble chromatin from MDA-MB-468/CshRNA, MDA-MB-468/xCTshRNA (C), BT-20/CshRNA and BT-20/xCTshRNA (D) cells was precipitated with anti-H3K9me2, anti-H3K9me3 or a control IgG. The final DNA samples were amplified by qPCR with pairs of primers for the MUC1 promoter region or control GAPDH promoter. The results (mean±SD of 3 determinations) are expressed as the relative fold enrichment compared with that obtained with the IgG control (CshRNA cells, assigned a value of 1). E. Genomic DNA from the indicated MDA-MB-468 (left) and BT-20 (right) cells was subjected to immunoprecipitation of methylated DNA (MeDIP) and the precipitates were analyzed by qPCR of the MUC1 gene promoter. The results (mean±SD of 3 determinations) are expressed as relative fold enrichment compared to that obtained from CshRNA expressing cells (assigned a value of 1).

    Article Snippet: Methylated DNA immunoprecipitation (MeDIP) assays DNA methylation analysis was performed using the Methylation DNA IP (MeDIP) kit (Active Motif) by immunoprecipitating and enriching for DNA fragments containing 5-mC.

    Techniques: DNA Methylation Assay, Multiple Displacement Amplification, Amplification, Real-time Polymerase Chain Reaction, Immunoprecipitation, Methylation, Methylated DNA Immunoprecipitation, Expressing

    DNA methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) MEDIP with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P

    Journal: Nucleic Acids Research

    Article Title: Targeted DNA methylation by homology-directed repair in mammalian cells. Transcription reshapes methylation on the repaired gene

    doi: 10.1093/nar/gkt920

    Figure Lengend Snippet: DNA methylation and chromatin modifications of the DSB region in cells exposed to α-amanitin during repair. ( A ) Location of Bcg, Rec1 and Rec2 primers, which recognize selectively recombinant GFP. Cassette I and II refer to Figure 1 . ( B ) MEDIP with anti-5mC antibodies of recombinant GFP gene. Clones 3 and 4 were treated with α-amanitin for 24 h as described in Figure 2 and sorted 5 days after I-SceI as described in ‘Materials and Methods’ section. Content of 5mC is higher in L cells compared with H cells, α-amanitin also increases the levels of 5mC in L cells and lowers them in H cells. The results are similar for both amplicons (REC1 and REC2). All data derive from three independent experiments performed in triplicate (mean ± SD; n = 9). Differences between treatments were tested for statistical significance using Student’s matched pairs t test: * P

    Article Snippet: Methylated DNA immunoprecipitation (MEDIP) was performed essentially as described ( ) except that 2 µg of antibody specific for 5mC (Abcam cat. # ab-124936) were used to precipitate methylated DNA from 5 µg of total genomic DNA.

    Techniques: DNA Methylation Assay, Recombinant, Methylated DNA Immunoprecipitation, Clone Assay

    DNA methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. MeDIP was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.

    Journal: Oncogene

    Article Title: The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer

    doi: 10.1038/onc.2010.269

    Figure Lengend Snippet: DNA methylation of SLIT2 promoter in prostate cancer ( a ) The SLIT2 promoter was enriched by 5-methylcytidine. MeDIP was performed in the LNCaP cells using an anti-5-methylcytidine antibody and IgG control. The IL-3 gene was used as a positive control and KIAA0079 as a negative control. ( b ) Methylation inhibitors reactivate SLIT2 expression. The LNCaP, PC3 and A549 cells were treated with 5 μM HDAC inhibitor SAHA and/or 5 μM DNA methylation inhibitor 5-Aza for 24 or 48hrs. Total RNA was isolated and analyzed by qRT-PCR. SLIT2 expression was normalized to GAPDH . Error bars represent mean ± SEM. ( c ) Detection of SLIT2 promoter region methylation in prostate tumor samples. DNA samples were bisulfite-modified and the SLIT2 promoter region was amplified. At least 5 clones per sample were subject to bisulfite sequencing. The circles indicate the CpG dinucleotides shown in the sequence chromatograph. The shades of gray indicate detection of methylated CpG in 20%, 40%, 60%, 80% or 100% of the clones. N is for normal, T for localized tumor, and M for Metastatic prostate tumors. An example sequence trace of one clone is shown at the bottom of the panel. Circled bases represent the CpG dinucleotides analyzed above.

    Article Snippet: MeDIP Methylated DNA immunoprecipitation (MeDIP) was performed in genomic DNA using an anti-5-methylcytidine antibody (BI-MECY_0100, Eurogentec) or IgG control (Santa Cruz) according to previously published protocols ( ).

    Techniques: DNA Methylation Assay, Methylated DNA Immunoprecipitation, Positive Control, Negative Control, Methylation, Expressing, Isolation, Quantitative RT-PCR, Modification, Amplification, Clone Assay, Methylation Sequencing, Sequencing

    Replicative efficiency of divergent mtDNA ES lines. CC9 mus , CC9 spretus , CC9 dunni and CC9 pahari ES cells were induced to differentiate into neural lineages over 21 days and were assessed at days 0 ( a ), 3 ( b ), 12 ( c ) and 21 ( d ) of differentiation for mtDNA copy number and ratios of 5mC and 5hmC. MtDNA copy number was assessed by real-time PCR. Levels of enrichment for 5mC and 5hmC were assessed by MeDIP using antibodies against 5mC and 5hmC, and real-time PCR across exon 2 of PolgA. The data are expressed as a ratio of mtDNA copy against 5mC/5hmC, where 5mC and 5hmC are indicative of DNA methylation and DNA demethylation, respectively. ** P

    Journal: Cell Death Discovery

    Article Title: Mitochondrial DNA haplotypes induce differential patterns of DNA methylation that result in differential chromosomal gene expression patterns

    doi: 10.1038/cddiscovery.2017.62

    Figure Lengend Snippet: Replicative efficiency of divergent mtDNA ES lines. CC9 mus , CC9 spretus , CC9 dunni and CC9 pahari ES cells were induced to differentiate into neural lineages over 21 days and were assessed at days 0 ( a ), 3 ( b ), 12 ( c ) and 21 ( d ) of differentiation for mtDNA copy number and ratios of 5mC and 5hmC. MtDNA copy number was assessed by real-time PCR. Levels of enrichment for 5mC and 5hmC were assessed by MeDIP using antibodies against 5mC and 5hmC, and real-time PCR across exon 2 of PolgA. The data are expressed as a ratio of mtDNA copy against 5mC/5hmC, where 5mC and 5hmC are indicative of DNA methylation and DNA demethylation, respectively. ** P

    Article Snippet: Immunoprecipitation of methylated DNA Immunoprecipitation of methylated DNA (MeDIP) was performed, as previously described., Briefly, 3 μ g of the sonicated DNA was immunoprecipitated with 2 μ g of either 5mC (Active Motif, Carlsbad, CA, USA) or 5hmC (Active Motif) at 4 °C overnight, and the immunoprecipitated DNA was purified using the Qiagen PCR Purification Kit (Qiagen).

    Techniques: Real-time Polymerase Chain Reaction, Methylated DNA Immunoprecipitation, DNA Methylation Assay