h3k27me3 Millipore Search Results


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  • 99
    Millipore h3k27me3 millipore antibodies
    Viral infection downregulates NDR1 expression in a type I IFN pathway-dependent manner. a Real-time PCR analysis of NDR1 mRNA in the peripheral blood from patients infected with RSV ( n = 77) and healthy control ( n = 40). b , c Real-time PCR ( b ) and immunoblot analysis ( c ) of NDR1 expression in peritoneal macrophages (PMs) infected with RSV, VSV, HSV, or MHV68. d , e Immunoblot analysis of NDR1 expression in PMs treated with IFNβ (100 IU ml −1 ) (d) , or with IFNα (100 IU ml −1 ) ( e ). f , g Immunoblot analysis of NDR1 expression in lysates of IFNαR +/+ and IFNαR −/ − ( f ) or STAT1 +/+ and STAT1 −/ − ( g ) mouse immortalized bone marrow-derived macrophages infected with VSV. h , i ChIP-qPCR analysis of the histone modification in NDR1 promoter with <t>H3K27me3</t> and H3K4me3 antibodies in lysates of Thp1 cells treated with VSV for 8 h ( h ) or with IFNα (100 IU ml −1 ) for 4 h ( i ). Data are mean ± SD and are representative of three independent experiments. Student’s t test was used for statistical calculation. * p
    H3k27me3 Millipore Antibodies, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me3 millipore
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    H3k27me3 Millipore, supplied by Millipore, used in various techniques. Bioz Stars score: 86/100, based on 465 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me3 upstate millipore
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    H3k27me3 Upstate Millipore, supplied by Millipore, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Active Motif millipore anti h3k27me3
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    Millipore Anti H3k27me3, supplied by Active Motif, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore ab24684 rabbit h3k27me3 millipore
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    Ab24684 Rabbit H3k27me3 Millipore, supplied by Millipore, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Merck KGaA anti h3k27me3 merck millipore antibody
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    Anti H3k27me3 Merck Millipore Antibody, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore anti h3k27me3 millipore antibody staining
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    Anti H3k27me3 Millipore Antibody Staining, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me2 millipore
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    H3k27me2 Millipore, supplied by Millipore, used in various techniques. Bioz Stars score: 86/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me1 millipore
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    H3k27me1 Millipore, supplied by Millipore, used in various techniques. Bioz Stars score: 86/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me1 millipore 07
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    H3k27me1 Millipore 07, 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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    Millipore millipore anti h3k27me1
    H3K4me3 and <t>H3K27me3</t> enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.
    Millipore Anti H3k27me1, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore anti h3k27me3
    Multiscale Chromatin and RNA Gene Regulatory Analyses of Control (Normoxic) and Hypoxic Arabidopsis Seedlings. (A) Schematic of the experiments performed. Seven-day–old seedlings were subjected to control (normoxic; 2NS, 9NS), hypoxic stress (2HS, 9HS), or reoxygenation after 2HS (R) conditions. 2NS is ZT16, and 9NS is ZT1, with 1-h extended darkness. Vertical arrows indicate time of harvest. ChIP was performed to evaluate genomic regions bound by Ser2P, the Histone 2 variant H2A.Z, modified Histone 3 (H3K4me3, <t>H3K27me3,</t> H3K9ac, and H3K14ac), and the ERF TF, HRE2. INTACT purified nuclei were used for the ATAC and purification of nRNA. Ribosome-associated mRNA was obtained by TRAP. (B) Individual replicate samples of nRNA, polyA RNA, and TRAP mRNA [TRAP] were compared by t-SNE. (C) to (E) Distributions of histone modifications/variants across genic regions (C) for the core HRG s ( n = 49; D) and cytosolic RP s ( n = 246; E). Read distributions (RPKM * 1,000) are plotted from 1 kb upstream to 1 kb downstream of gene units defined by the TSS and TES.
    Anti H3k27me3, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 2095 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Merck KGaA h3k27me3
    Genome-wide changes in H3K4me3 and <t>H3K27me3</t> enrichment following NK cells treated with GSK-J4. A , average coverage of ATAC-seq reads around the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from ATAC-seq over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. B and C , average H3K4me3 and H3K27me3 coverage across the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from H3K27me3 and H3K4me3 over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. D and E , representative RNA-seq and ChIP-seq coverage profiles of H3K4me3, H3K27me3 across the IFNG locus, and the TNF locus. For each gene, the coverage profile was normalized by dividing the average coverage in that gene. Red , DMSO; blue , GSK-J4-treated. F , the ChIP-PCR results confirm the ChIP-seq results at the IFNG and LTA promoters. The data shown are for two donors with triplicate measurements each.
    H3k27me3, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 92/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore acid extraction buffer
    Genome-wide changes in H3K4me3 and <t>H3K27me3</t> enrichment following NK cells treated with GSK-J4. A , average coverage of ATAC-seq reads around the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from ATAC-seq over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. B and C , average H3K4me3 and H3K27me3 coverage across the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from H3K27me3 and H3K4me3 over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. D and E , representative RNA-seq and ChIP-seq coverage profiles of H3K4me3, H3K27me3 across the IFNG locus, and the TNF locus. For each gene, the coverage profile was normalized by dividing the average coverage in that gene. Red , DMSO; blue , GSK-J4-treated. F , the ChIP-PCR results confirm the ChIP-seq results at the IFNG and LTA promoters. The data shown are for two donors with triplicate measurements each.
    Acid Extraction Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore h3k27me3 07 449 antibody
    Genome-wide changes in H3K4me3 and <t>H3K27me3</t> enrichment following NK cells treated with GSK-J4. A , average coverage of ATAC-seq reads around the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from ATAC-seq over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. B and C , average H3K4me3 and H3K27me3 coverage across the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from H3K27me3 and H3K4me3 over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. D and E , representative RNA-seq and ChIP-seq coverage profiles of H3K4me3, H3K27me3 across the IFNG locus, and the TNF locus. For each gene, the coverage profile was normalized by dividing the average coverage in that gene. Red , DMSO; blue , GSK-J4-treated. F , the ChIP-PCR results confirm the ChIP-seq results at the IFNG and LTA promoters. The data shown are for two donors with triplicate measurements each.
    H3k27me3 07 449 Antibody, supplied by Millipore, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Viral infection downregulates NDR1 expression in a type I IFN pathway-dependent manner. a Real-time PCR analysis of NDR1 mRNA in the peripheral blood from patients infected with RSV ( n = 77) and healthy control ( n = 40). b , c Real-time PCR ( b ) and immunoblot analysis ( c ) of NDR1 expression in peritoneal macrophages (PMs) infected with RSV, VSV, HSV, or MHV68. d , e Immunoblot analysis of NDR1 expression in PMs treated with IFNβ (100 IU ml −1 ) (d) , or with IFNα (100 IU ml −1 ) ( e ). f , g Immunoblot analysis of NDR1 expression in lysates of IFNαR +/+ and IFNαR −/ − ( f ) or STAT1 +/+ and STAT1 −/ − ( g ) mouse immortalized bone marrow-derived macrophages infected with VSV. h , i ChIP-qPCR analysis of the histone modification in NDR1 promoter with H3K27me3 and H3K4me3 antibodies in lysates of Thp1 cells treated with VSV for 8 h ( h ) or with IFNα (100 IU ml −1 ) for 4 h ( i ). Data are mean ± SD and are representative of three independent experiments. Student’s t test was used for statistical calculation. * p

    Journal: Nature Communications

    Article Title: Downregulated NDR1 protein kinase inhibits innate immune response by initiating an miR146a-STAT1 feedback loop

    doi: 10.1038/s41467-018-05176-7

    Figure Lengend Snippet: Viral infection downregulates NDR1 expression in a type I IFN pathway-dependent manner. a Real-time PCR analysis of NDR1 mRNA in the peripheral blood from patients infected with RSV ( n = 77) and healthy control ( n = 40). b , c Real-time PCR ( b ) and immunoblot analysis ( c ) of NDR1 expression in peritoneal macrophages (PMs) infected with RSV, VSV, HSV, or MHV68. d , e Immunoblot analysis of NDR1 expression in PMs treated with IFNβ (100 IU ml −1 ) (d) , or with IFNα (100 IU ml −1 ) ( e ). f , g Immunoblot analysis of NDR1 expression in lysates of IFNαR +/+ and IFNαR −/ − ( f ) or STAT1 +/+ and STAT1 −/ − ( g ) mouse immortalized bone marrow-derived macrophages infected with VSV. h , i ChIP-qPCR analysis of the histone modification in NDR1 promoter with H3K27me3 and H3K4me3 antibodies in lysates of Thp1 cells treated with VSV for 8 h ( h ) or with IFNα (100 IU ml −1 ) for 4 h ( i ). Data are mean ± SD and are representative of three independent experiments. Student’s t test was used for statistical calculation. * p

    Article Snippet: After sonication, DNA was immunoprecipitated overnight at 4 °C with 2 µg of an anti-NF-κB antibody, anti-STAT1 antibody, anti-H3K4me3 antibody, anti-H3K27me3 antibody or negative control immunoglobulin, and protein A/G beads or antiflag (M2) beads (Sigma-Aldrich).

    Techniques: Infection, Expressing, Real-time Polymerase Chain Reaction, Derivative Assay, Chromatin Immunoprecipitation, Modification

    Results of RIP and ChIP assays for primary HDFs. (A) Relative expression of EZH2 in heat-treated HDFs. (B) RIP analysis was performed using antibodies against EZH2 and IgG. (C) pc-EZH2 and si-EZH2 were transfected into HDFs. (D) ChIP analysis was performed using antibodies against H3K27me3 and IgG. (E) Relative expression of LET in HDFs transfected with pc-EZH2 or si-EZH2. (F) Correlation of LET and EZH2 expression in burn tissues from patients. * P

    Journal: International Journal of Molecular Medicine

    Article Title: EZH2-mediated suppression of lncRNA-LET promotes cell apoptosis and inhibits the proliferation of post-burn skin fibroblasts

    doi: 10.3892/ijmm.2018.3425

    Figure Lengend Snippet: Results of RIP and ChIP assays for primary HDFs. (A) Relative expression of EZH2 in heat-treated HDFs. (B) RIP analysis was performed using antibodies against EZH2 and IgG. (C) pc-EZH2 and si-EZH2 were transfected into HDFs. (D) ChIP analysis was performed using antibodies against H3K27me3 and IgG. (E) Relative expression of LET in HDFs transfected with pc-EZH2 or si-EZH2. (F) Correlation of LET and EZH2 expression in burn tissues from patients. * P

    Article Snippet: Firstly, cross-linked chromatin was sonicated into fragments in the size range 200–1,000 bp, and the fragments were immunoprecipitated using H3K27me3 antibody (dilution 1:500; SAB4800015; Sigma-Aldrich; Merck KGaA).

    Techniques: Chromatin Immunoprecipitation, Expressing, Transfection

    Model for the H3K27me3 dependent EZH2-LET interaction mechanism. Both H3K27me3 and EZH2-LET interaction were essential for expression of lncRNA LET, and the downstream proteins related to cell proliferation and apoptosis. Three methylation sites of EZH2 at H3K27me3 promoter are presented by three yellow balls. EZH2-catalyzed H3K27me3 trimethylation inhibits lncRNA-LET expression and promotes cell apoptosis. H3K27me3, histone H3 lysine 27 trimethylation; EZH2, enhancer of zeste homolog 2; LET, low expression in tumor; lncRNA, long non-coding RNA; PRC2, polycomb repressive complex 2; Bax, Bcl-2-associated X protein; Bcl-2, B-cell lymphoma 2.

    Journal: International Journal of Molecular Medicine

    Article Title: EZH2-mediated suppression of lncRNA-LET promotes cell apoptosis and inhibits the proliferation of post-burn skin fibroblasts

    doi: 10.3892/ijmm.2018.3425

    Figure Lengend Snippet: Model for the H3K27me3 dependent EZH2-LET interaction mechanism. Both H3K27me3 and EZH2-LET interaction were essential for expression of lncRNA LET, and the downstream proteins related to cell proliferation and apoptosis. Three methylation sites of EZH2 at H3K27me3 promoter are presented by three yellow balls. EZH2-catalyzed H3K27me3 trimethylation inhibits lncRNA-LET expression and promotes cell apoptosis. H3K27me3, histone H3 lysine 27 trimethylation; EZH2, enhancer of zeste homolog 2; LET, low expression in tumor; lncRNA, long non-coding RNA; PRC2, polycomb repressive complex 2; Bax, Bcl-2-associated X protein; Bcl-2, B-cell lymphoma 2.

    Article Snippet: Firstly, cross-linked chromatin was sonicated into fragments in the size range 200–1,000 bp, and the fragments were immunoprecipitated using H3K27me3 antibody (dilution 1:500; SAB4800015; Sigma-Aldrich; Merck KGaA).

    Techniques: Expressing, Methylation

    H3K4me3 and H3K27me3 enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.

    Journal: PLoS ONE

    Article Title: Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

    doi: 10.1371/journal.pone.0015651

    Figure Lengend Snippet: H3K4me3 and H3K27me3 enrichment profiles in ZF4 cells. (A) Distinct H3K4me3 and H3K27me3 enrichment profiles on indicated genomic regions. Genomic positioning is indicated by nucleotide number of the first (5′) and last (3′) probe in the tiled region. Gene names or accession numbers as well as their genomic position are shown in blue. (B) 2-D scatter plot of averaged MaxSixty values for H3K4me3 vs. H3K27me3 log 2 signal intensities. Data points (all points being shown in gray) were colored to visualize classification according to peak calling highlighting H3K4me3-enriched promoters (purple; N = 6315), H3K27me3-enriched promoters (green; N = 1079) and H3K4me3/K27me3-co-enriched promoters (blue; N = 2120). Red line is the regression line through all data points. (C) Venn diagram analysis of H3K4me3 and H3K27me3 genes.

    Article Snippet: Enriched GO terms with gene list among expressed and non-expressed genes marked by H3K4me3, H3K27me3 or both marks. (XLS) Click here for additional data file.

    Techniques:

    Distribution of H3K4me3 and H3K27me3 on promoters. Metagene analysis of the distribution of H3K4me3 and H3K27me3 occupancy on (A) H3K4me3-only, (B) H3K27me3-only and (C) H3K4me3/K27me3 tiled regions, relative to the TSS (red vertical bar). (D) Sequential ChIP analysis of H3K4me3 and H3K27me3 co-enrichment on the sox3 , sox2 promoters and on bactin1 , downstream of the coding region. Panels on the left show results from the first ChIP using antibodies indicated on the x-axis. The graph on the right shows results of the re-ChIP experiment as indicated on the x-axis.

    Journal: PLoS ONE

    Article Title: Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

    doi: 10.1371/journal.pone.0015651

    Figure Lengend Snippet: Distribution of H3K4me3 and H3K27me3 on promoters. Metagene analysis of the distribution of H3K4me3 and H3K27me3 occupancy on (A) H3K4me3-only, (B) H3K27me3-only and (C) H3K4me3/K27me3 tiled regions, relative to the TSS (red vertical bar). (D) Sequential ChIP analysis of H3K4me3 and H3K27me3 co-enrichment on the sox3 , sox2 promoters and on bactin1 , downstream of the coding region. Panels on the left show results from the first ChIP using antibodies indicated on the x-axis. The graph on the right shows results of the re-ChIP experiment as indicated on the x-axis.

    Article Snippet: Enriched GO terms with gene list among expressed and non-expressed genes marked by H3K4me3, H3K27me3 or both marks. (XLS) Click here for additional data file.

    Techniques: Chromatin Immunoprecipitation

    Reproducibility of zebrafish ChIP-chip experiments. (A) Two-dimensional scatter plots of MaxSixty values for H3K4me3 and H3K27me3 log 2 signal intensities detected in each of two ChIP-chip replicates from ZF4 cells. Correlation coefficient (R) and regression line are shown. (B) H3K4me3 and H3K27me3 profiles detected by ChIP-chip in two independent replicates through 310 kb of zebrafish chromosome 10. Data are expressed as log 2 ChIP/input ratios. Position of methylation peaks are shown as blue horizontal bars. Tracks representing primary transcripts and tiled regions are also shown. Primary transcripts included in the region are as follows: 1) sin2 ; 2) NM_001003421; 3) NM_200663; 4) NM_001008616; 5) ENSDART00000081978; 6) ripply3 , 7) ENSDART00000081992; 8) dyrk1aa ; 9) ENSDART00000058411; 10) ENSDART00000088605; 11) NM_001037708; 12) hyou1 ; 13) hist2h2l ; 14) znf259 . Red bars in the H3K4me3 tracks indicate probes with out-of-scale signal intensity.

    Journal: PLoS ONE

    Article Title: Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

    doi: 10.1371/journal.pone.0015651

    Figure Lengend Snippet: Reproducibility of zebrafish ChIP-chip experiments. (A) Two-dimensional scatter plots of MaxSixty values for H3K4me3 and H3K27me3 log 2 signal intensities detected in each of two ChIP-chip replicates from ZF4 cells. Correlation coefficient (R) and regression line are shown. (B) H3K4me3 and H3K27me3 profiles detected by ChIP-chip in two independent replicates through 310 kb of zebrafish chromosome 10. Data are expressed as log 2 ChIP/input ratios. Position of methylation peaks are shown as blue horizontal bars. Tracks representing primary transcripts and tiled regions are also shown. Primary transcripts included in the region are as follows: 1) sin2 ; 2) NM_001003421; 3) NM_200663; 4) NM_001008616; 5) ENSDART00000081978; 6) ripply3 , 7) ENSDART00000081992; 8) dyrk1aa ; 9) ENSDART00000058411; 10) ENSDART00000088605; 11) NM_001037708; 12) hyou1 ; 13) hist2h2l ; 14) znf259 . Red bars in the H3K4me3 tracks indicate probes with out-of-scale signal intensity.

    Article Snippet: Enriched GO terms with gene list among expressed and non-expressed genes marked by H3K4me3, H3K27me3 or both marks. (XLS) Click here for additional data file.

    Techniques: Chromatin Immunoprecipitation, Methylation

    Quantitative PCR validation of ChIP-chip data. (A) ChIP-on-chip profiles of H3K4me3 and H3K27me3 enrichment on indicated genes. Position of primary transcripts and TSS (arrow) are shown. (B) ChIP-qPCR analysis of H3K4me3 and H3K27me3 enrichment on the same genes as in (A) from separate duplicate ChIPs. ChIP DNA was not WGA amplified prior to PCR. Position of amplicons and primer sequences for each gene are shown in Table S3 . Note the correlation between ChIP- chip and ChIP-qPCR data.

    Journal: PLoS ONE

    Article Title: Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

    doi: 10.1371/journal.pone.0015651

    Figure Lengend Snippet: Quantitative PCR validation of ChIP-chip data. (A) ChIP-on-chip profiles of H3K4me3 and H3K27me3 enrichment on indicated genes. Position of primary transcripts and TSS (arrow) are shown. (B) ChIP-qPCR analysis of H3K4me3 and H3K27me3 enrichment on the same genes as in (A) from separate duplicate ChIPs. ChIP DNA was not WGA amplified prior to PCR. Position of amplicons and primer sequences for each gene are shown in Table S3 . Note the correlation between ChIP- chip and ChIP-qPCR data.

    Article Snippet: Enriched GO terms with gene list among expressed and non-expressed genes marked by H3K4me3, H3K27me3 or both marks. (XLS) Click here for additional data file.

    Techniques: Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation, Whole Genome Amplification, Amplification, Polymerase Chain Reaction

    Genes marked by H3K4me3 and/or H3K27me3 are linked to distinct functional GO terms. (A) GO term enrichment of genes containing H3K4me3, H3K27me3 or H3K4/K27me3 promoters in ZF4 cells. The twelve most significant GO terms are shown as a function of significance from bottom (highest significance) to top. (B) Representation of all enriched GO terms among H3K4/K27me3 genes. All enriched GO terms are listed in Table S1 . (C) H3K4me3 and H3K27me3 enrichment profiles on the developmentally regulated hoxc locus, expressed as log 2 ChIP/Input (y axis).

    Journal: PLoS ONE

    Article Title: Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

    doi: 10.1371/journal.pone.0015651

    Figure Lengend Snippet: Genes marked by H3K4me3 and/or H3K27me3 are linked to distinct functional GO terms. (A) GO term enrichment of genes containing H3K4me3, H3K27me3 or H3K4/K27me3 promoters in ZF4 cells. The twelve most significant GO terms are shown as a function of significance from bottom (highest significance) to top. (B) Representation of all enriched GO terms among H3K4/K27me3 genes. All enriched GO terms are listed in Table S1 . (C) H3K4me3 and H3K27me3 enrichment profiles on the developmentally regulated hoxc locus, expressed as log 2 ChIP/Input (y axis).

    Article Snippet: Enriched GO terms with gene list among expressed and non-expressed genes marked by H3K4me3, H3K27me3 or both marks. (XLS) Click here for additional data file.

    Techniques: Functional Assay, Chromatin Immunoprecipitation

    Effects of E-cadherin transgene expression on X-inactivation status. A) Morphology of EpiSCs with or without induction of E-cadherin upon addition of doxycycline (-Dox and +Dox). B) The X-inactivation status of Nanog-induced (NaIN5) or E-cadherin-induced (EIN6) EpiSCs. The Nanog or E-cadherin transgene was induced with doxycycline for 2 days with or without Activin and Fgf2 (+AF or –AF) and stained with H3K27me3 (shown in green) and Oct3/4 (shown in red). White arrowheads indicate inactive X chromosome (XCI)-negative cells. C) Measurement of the ratio of XCI-negative and -positive cells in Figure 3B . Only Oct3/4-positive cells were counted in each case. Note that NaIN and EIN cells maintained 100% XCI in EpiSC medium without doxycycline (data not shown). D) E-cadherin induced EpiSCs lost XCI in injected blastocysts cultured for 36 h. EpiSCs induced by E-cadherin for 2 days were injected into blastocysts with the single-injection protocol. The embryos were then cultured for 36 h followed by immunostaining with H3K27me3 antibody to estimate reprogramming events in developing embryos. EGFP-positive cells (green) and H3K27me3-positive (red) cells were counted in injected embryos. E) Measurement of the ratio of XCI-positive and negative cells in Figure 3D . Only GFP positive cell were counted (p

    Journal: PLoS ONE

    Article Title: E-Cadherin Promotes Incorporation of Mouse Epiblast Stem Cells into Normal Development

    doi: 10.1371/journal.pone.0045220

    Figure Lengend Snippet: Effects of E-cadherin transgene expression on X-inactivation status. A) Morphology of EpiSCs with or without induction of E-cadherin upon addition of doxycycline (-Dox and +Dox). B) The X-inactivation status of Nanog-induced (NaIN5) or E-cadherin-induced (EIN6) EpiSCs. The Nanog or E-cadherin transgene was induced with doxycycline for 2 days with or without Activin and Fgf2 (+AF or –AF) and stained with H3K27me3 (shown in green) and Oct3/4 (shown in red). White arrowheads indicate inactive X chromosome (XCI)-negative cells. C) Measurement of the ratio of XCI-negative and -positive cells in Figure 3B . Only Oct3/4-positive cells were counted in each case. Note that NaIN and EIN cells maintained 100% XCI in EpiSC medium without doxycycline (data not shown). D) E-cadherin induced EpiSCs lost XCI in injected blastocysts cultured for 36 h. EpiSCs induced by E-cadherin for 2 days were injected into blastocysts with the single-injection protocol. The embryos were then cultured for 36 h followed by immunostaining with H3K27me3 antibody to estimate reprogramming events in developing embryos. EGFP-positive cells (green) and H3K27me3-positive (red) cells were counted in injected embryos. E) Measurement of the ratio of XCI-positive and negative cells in Figure 3D . Only GFP positive cell were counted (p

    Article Snippet: Cells were cultured for the indicated times in each experiment on fibronectin-coated ibidi-treated chamber slides (Nippon Genetics Co., Ltd.), fixed with 4% paraformaldehyde, and stained with the following primary antibodies: anti-E-cadherin (kindly provided by Dr. Masatoshi Takeichi), H3K27me3 antibody (1∶2000 dilution, #07-449; Millipore Corporation), and anti-Oct3/4 (1∶2000 dilution, C-10; Santa Cruz Biotechnology Inc.).

    Techniques: Expressing, Staining, Injection, Cell Culture, Immunostaining

    Multiscale Chromatin and RNA Gene Regulatory Analyses of Control (Normoxic) and Hypoxic Arabidopsis Seedlings. (A) Schematic of the experiments performed. Seven-day–old seedlings were subjected to control (normoxic; 2NS, 9NS), hypoxic stress (2HS, 9HS), or reoxygenation after 2HS (R) conditions. 2NS is ZT16, and 9NS is ZT1, with 1-h extended darkness. Vertical arrows indicate time of harvest. ChIP was performed to evaluate genomic regions bound by Ser2P, the Histone 2 variant H2A.Z, modified Histone 3 (H3K4me3, H3K27me3, H3K9ac, and H3K14ac), and the ERF TF, HRE2. INTACT purified nuclei were used for the ATAC and purification of nRNA. Ribosome-associated mRNA was obtained by TRAP. (B) Individual replicate samples of nRNA, polyA RNA, and TRAP mRNA [TRAP] were compared by t-SNE. (C) to (E) Distributions of histone modifications/variants across genic regions (C) for the core HRG s ( n = 49; D) and cytosolic RP s ( n = 246; E). Read distributions (RPKM * 1,000) are plotted from 1 kb upstream to 1 kb downstream of gene units defined by the TSS and TES.

    Journal: The Plant Cell

    Article Title: Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress [OPEN]

    doi: 10.1105/tpc.19.00463

    Figure Lengend Snippet: Multiscale Chromatin and RNA Gene Regulatory Analyses of Control (Normoxic) and Hypoxic Arabidopsis Seedlings. (A) Schematic of the experiments performed. Seven-day–old seedlings were subjected to control (normoxic; 2NS, 9NS), hypoxic stress (2HS, 9HS), or reoxygenation after 2HS (R) conditions. 2NS is ZT16, and 9NS is ZT1, with 1-h extended darkness. Vertical arrows indicate time of harvest. ChIP was performed to evaluate genomic regions bound by Ser2P, the Histone 2 variant H2A.Z, modified Histone 3 (H3K4me3, H3K27me3, H3K9ac, and H3K14ac), and the ERF TF, HRE2. INTACT purified nuclei were used for the ATAC and purification of nRNA. Ribosome-associated mRNA was obtained by TRAP. (B) Individual replicate samples of nRNA, polyA RNA, and TRAP mRNA [TRAP] were compared by t-SNE. (C) to (E) Distributions of histone modifications/variants across genic regions (C) for the core HRG s ( n = 49; D) and cytosolic RP s ( n = 246; E). Read distributions (RPKM * 1,000) are plotted from 1 kb upstream to 1 kb downstream of gene units defined by the TSS and TES.

    Article Snippet: Three-hundred microliters of the input chromatin (1 mL for HRE2) was incubated with 3 μL of undiluted anti-H3K4me3 (cat. no. ab8580; Abcam), anti-H3K27me3 (cat. no. 07-449; EMD Millipore), anti-H3K9ac (cat. no. ab4441; Abcam), anti-H3K14ac (cat. no. ab52946; Abcam), anti-p-CTD RNAPII (cat. no. ab5095; Abcam), anti-FLAG (cat. no. F1804; Sigma-Aldrich; 1:100 dilution), or anti-HA (cat. no. h3663; Sigma-Aldrich; 1:333 dilution) antibodies for 4 h (overnight for HRE2) while rocking at 4°C.

    Techniques: Chromatin Immunoprecipitation, Variant Assay, Modification, Purification

    Genome-wide changes in H3K4me3 and H3K27me3 enrichment following NK cells treated with GSK-J4. A , average coverage of ATAC-seq reads around the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from ATAC-seq over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. B and C , average H3K4me3 and H3K27me3 coverage across the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from H3K27me3 and H3K4me3 over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. D and E , representative RNA-seq and ChIP-seq coverage profiles of H3K4me3, H3K27me3 across the IFNG locus, and the TNF locus. For each gene, the coverage profile was normalized by dividing the average coverage in that gene. Red , DMSO; blue , GSK-J4-treated. F , the ChIP-PCR results confirm the ChIP-seq results at the IFNG and LTA promoters. The data shown are for two donors with triplicate measurements each.

    Journal: The Journal of Biological Chemistry

    Article Title: Inhibition of histone H3K27 demethylases selectively modulates inflammatory phenotypes of natural killer cells

    doi: 10.1074/jbc.RA117.000698

    Figure Lengend Snippet: Genome-wide changes in H3K4me3 and H3K27me3 enrichment following NK cells treated with GSK-J4. A , average coverage of ATAC-seq reads around the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from ATAC-seq over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. B and C , average H3K4me3 and H3K27me3 coverage across the TSS of all reference genes following 24 h of DMSO and GSK-J4 treatment. Coverage plots showing the reads from H3K27me3 and H3K4me3 over the down-regulated ( bottom left panel ) and up-regulated genes ( bottom right panel ) are also shown. D and E , representative RNA-seq and ChIP-seq coverage profiles of H3K4me3, H3K27me3 across the IFNG locus, and the TNF locus. For each gene, the coverage profile was normalized by dividing the average coverage in that gene. Red , DMSO; blue , GSK-J4-treated. F , the ChIP-PCR results confirm the ChIP-seq results at the IFNG and LTA promoters. The data shown are for two donors with triplicate measurements each.

    Article Snippet: Each lysate was immunoprecipitated with 10 μg of the following antibodies: H3K4me3 (Merck Millipore) and H3K27me3 (Merck Millipore).

    Techniques: Genome Wide, RNA Sequencing Assay, Chromatin Immunoprecipitation, Polymerase Chain Reaction