input dna  (Millipore)


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    Name:
    Deoxyribonucleic acid
    Description:
    Human placental DNA is isolated from donor placenta but will contain some maternal DNA The DNA fragments are sonicated to produce fragments of consistent size
    Catalog Number:
    d3287
    Price:
    None
    Applications:
    Sonicated Deoxyribonucleic acid, single stranded from human placenta, was used as blocking agent in Southern hybridization of DNA from human papillomavirus (HPV) positive SiHa, HeLa and CaSki cell-lines. It was used as standard in GC/MS analysis of exocyclic DNA adducts.
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    Structured Review

    Millipore input dna
    The levels of H3K27me3 at promoter regions in GMPs. Visualization of ChIP-seq data of the H3K27me3 levels of several developmental regulator genes ( Hoxd locus, Gata4 , and Pax5 ), tumor suppressor genes ( Cdkn2a and Cdkn2b ) and oncogenes ( Hmga2 and Pbx3 ) in GMPs from WT, Tet2 KD/KD , Ezh2 Δ/Δ , and Tet2 KD/KD Ezh2 Δ/Δ mice at 4 mo after transplantation using the Integrative Genomics Viewer (IGV). Schematic diagram of these gene loci indicates their genomic structures. Exons and untranslated regions are demarcated by large and small black boxes, respectively. Data of ChIP analyses at the promoters of selected genes are also depicted. Quantitative ChIP analyses of GMPs from WT and Ezh2 Δ/Δ mice at 6 mo after transplantation were performed. The relative amounts of <t>immunoprecipitated</t> <t>DNA</t> are depicted as a percentage of input DNA. N.D. indicates not detected. The data are shown as the mean ± SEM for triplicate analyses. Regions amplified from the precipitated DNA by site-specific quantitative PCR are indicated by arrows. *, P
    Human placental DNA is isolated from donor placenta but will contain some maternal DNA The DNA fragments are sonicated to produce fragments of consistent size
    https://www.bioz.com/result/input dna/product/Millipore
    Average 99 stars, based on 126 article reviews
    Price from $9.99 to $1999.99
    input dna - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders"

    Article Title: Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders

    Journal: The Journal of Experimental Medicine

    doi: 10.1084/jem.20131144

    The levels of H3K27me3 at promoter regions in GMPs. Visualization of ChIP-seq data of the H3K27me3 levels of several developmental regulator genes ( Hoxd locus, Gata4 , and Pax5 ), tumor suppressor genes ( Cdkn2a and Cdkn2b ) and oncogenes ( Hmga2 and Pbx3 ) in GMPs from WT, Tet2 KD/KD , Ezh2 Δ/Δ , and Tet2 KD/KD Ezh2 Δ/Δ mice at 4 mo after transplantation using the Integrative Genomics Viewer (IGV). Schematic diagram of these gene loci indicates their genomic structures. Exons and untranslated regions are demarcated by large and small black boxes, respectively. Data of ChIP analyses at the promoters of selected genes are also depicted. Quantitative ChIP analyses of GMPs from WT and Ezh2 Δ/Δ mice at 6 mo after transplantation were performed. The relative amounts of immunoprecipitated DNA are depicted as a percentage of input DNA. N.D. indicates not detected. The data are shown as the mean ± SEM for triplicate analyses. Regions amplified from the precipitated DNA by site-specific quantitative PCR are indicated by arrows. *, P
    Figure Legend Snippet: The levels of H3K27me3 at promoter regions in GMPs. Visualization of ChIP-seq data of the H3K27me3 levels of several developmental regulator genes ( Hoxd locus, Gata4 , and Pax5 ), tumor suppressor genes ( Cdkn2a and Cdkn2b ) and oncogenes ( Hmga2 and Pbx3 ) in GMPs from WT, Tet2 KD/KD , Ezh2 Δ/Δ , and Tet2 KD/KD Ezh2 Δ/Δ mice at 4 mo after transplantation using the Integrative Genomics Viewer (IGV). Schematic diagram of these gene loci indicates their genomic structures. Exons and untranslated regions are demarcated by large and small black boxes, respectively. Data of ChIP analyses at the promoters of selected genes are also depicted. Quantitative ChIP analyses of GMPs from WT and Ezh2 Δ/Δ mice at 6 mo after transplantation were performed. The relative amounts of immunoprecipitated DNA are depicted as a percentage of input DNA. N.D. indicates not detected. The data are shown as the mean ± SEM for triplicate analyses. Regions amplified from the precipitated DNA by site-specific quantitative PCR are indicated by arrows. *, P

    Techniques Used: Chromatin Immunoprecipitation, Mouse Assay, Transplantation Assay, Immunoprecipitation, Amplification, Real-time Polymerase Chain Reaction

    2) Product Images from "Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore"

    Article Title: Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore

    Journal: The EMBO Journal

    doi: 10.1038/emboj.2010.329

    Active centromere chromatin displays the signature of elongating RNA polymerase. ( A ) Schematic of the HAC, derived from Nakano et al (2008) , indicating the synthetic alphoid tetO array (green: tetO; white: CENP-B box) and the HAC vector with YAC and BAC cassettes and the blasticidin (Bsr) resistance marker. The region of the alphoid tetO array analysed by ChIP is indicated by green line. ( B ) ChIP analysis in AB2.2.18.21 cells using antibodies of the indicated reactivity. The synthetic (alphoid tetO ) centromere, endogenous chromosome 21 α21-I satellite DNA (alphoid chr.21 ), the 5S rDNA loci and the Bsr gene on the HAC vector were assessed. Data represent the mean and s.d. of three independent ChIP experiments. Note the different scaling of individual panels reflecting different efficiencies of individual antibodies. ( C ) Real-time RT–PCR analysis of synthetic HAC centromere (alphoid tetO ), actively transcribed Bsr marker and endogenous chromosome 21 satellite (alphoid chr.21 ). Expression data are normalized to the copy number of the genomic regions and β-actin mRNA levels (see Materials and methods) and displayed as arbitrary numbers. Data represent the mean and s.e.m. of three independent experiments. Note the log scale.
    Figure Legend Snippet: Active centromere chromatin displays the signature of elongating RNA polymerase. ( A ) Schematic of the HAC, derived from Nakano et al (2008) , indicating the synthetic alphoid tetO array (green: tetO; white: CENP-B box) and the HAC vector with YAC and BAC cassettes and the blasticidin (Bsr) resistance marker. The region of the alphoid tetO array analysed by ChIP is indicated by green line. ( B ) ChIP analysis in AB2.2.18.21 cells using antibodies of the indicated reactivity. The synthetic (alphoid tetO ) centromere, endogenous chromosome 21 α21-I satellite DNA (alphoid chr.21 ), the 5S rDNA loci and the Bsr gene on the HAC vector were assessed. Data represent the mean and s.d. of three independent ChIP experiments. Note the different scaling of individual panels reflecting different efficiencies of individual antibodies. ( C ) Real-time RT–PCR analysis of synthetic HAC centromere (alphoid tetO ), actively transcribed Bsr marker and endogenous chromosome 21 satellite (alphoid chr.21 ). Expression data are normalized to the copy number of the genomic regions and β-actin mRNA levels (see Materials and methods) and displayed as arbitrary numbers. Data represent the mean and s.e.m. of three independent experiments. Note the log scale.

    Techniques Used: HAC Assay, Derivative Assay, Plasmid Preparation, BAC Assay, Marker, Chromatin Immunoprecipitation, Quantitative RT-PCR, Expressing

    3) Product Images from "Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii"

    Article Title: Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky373

    TgAP2X-5 depletion prevents TgAP2XI-5 binding to a number of promoters. ( A ) ChIP-on-chip data are represented as the log 2 ratio of the hybridization signal given by DNA immunoprecipitated over the signal given by the non-enriched input DNA. The log 2 ratio of each oligonucleotide present on the tiled microarray has been plotted at the respective genomic position. Genes above the horizontal axis are encoded the forward strand whereas those below are encoded the reverse strand. The scale of the Y -axis was kept identical for all representation to allow the comparison of signals. TgAP2XI-5 ChIP-chip assay is represented for the TgAP2XI-5 protein in the parental strain (RH ΔhxgprtΔku80 , green, negative control) or TgAP2XI-5 tagged strain (red, positive control) or TgAP2XI-5 tagged in the iKD TgAP2X-5 strain in presence of ATc (orange). The associated peaks identified by the mPeak algorithm are also provided. A portion of the Toxoplasma gondii chromosome III is represented. The boxed promoter presents a lower enrichment of TgAP2XI-5 in the iKD TgAP2X-5 strain in presence of ATc. ( B ) Representation of the ChIP-chip experiments for a portion of chromosome IV which encompasses the TgROP15 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( C ) Representation of the ChIP-chip experiments for a portion of chromosome III which encompasses the TgROP24 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( D ) Quantitative PCR was performed on the TgAP2XI-5 ChIP assays performed in the iKD TgAP2X-5/TgAP2XI-5 strain (orange), iKD TgAP2X-5 complemented/TgAP2XI-5 strain (yellow), TgAP2XI-5-tagged strain (red) and parental strain (negative control, green). Amplification was carried out on regions within the promoter of each of the six genes listed. The enrichment for corresponding ChIP DNA samples is presented as a percentage of INPUT for each target.
    Figure Legend Snippet: TgAP2X-5 depletion prevents TgAP2XI-5 binding to a number of promoters. ( A ) ChIP-on-chip data are represented as the log 2 ratio of the hybridization signal given by DNA immunoprecipitated over the signal given by the non-enriched input DNA. The log 2 ratio of each oligonucleotide present on the tiled microarray has been plotted at the respective genomic position. Genes above the horizontal axis are encoded the forward strand whereas those below are encoded the reverse strand. The scale of the Y -axis was kept identical for all representation to allow the comparison of signals. TgAP2XI-5 ChIP-chip assay is represented for the TgAP2XI-5 protein in the parental strain (RH ΔhxgprtΔku80 , green, negative control) or TgAP2XI-5 tagged strain (red, positive control) or TgAP2XI-5 tagged in the iKD TgAP2X-5 strain in presence of ATc (orange). The associated peaks identified by the mPeak algorithm are also provided. A portion of the Toxoplasma gondii chromosome III is represented. The boxed promoter presents a lower enrichment of TgAP2XI-5 in the iKD TgAP2X-5 strain in presence of ATc. ( B ) Representation of the ChIP-chip experiments for a portion of chromosome IV which encompasses the TgROP15 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( C ) Representation of the ChIP-chip experiments for a portion of chromosome III which encompasses the TgROP24 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( D ) Quantitative PCR was performed on the TgAP2XI-5 ChIP assays performed in the iKD TgAP2X-5/TgAP2XI-5 strain (orange), iKD TgAP2X-5 complemented/TgAP2XI-5 strain (yellow), TgAP2XI-5-tagged strain (red) and parental strain (negative control, green). Amplification was carried out on regions within the promoter of each of the six genes listed. The enrichment for corresponding ChIP DNA samples is presented as a percentage of INPUT for each target.

    Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Hybridization, Immunoprecipitation, Microarray, Negative Control, Positive Control, Real-time Polymerase Chain Reaction, Amplification

    4) Product Images from "Effects of Sulforaphane and 3,3?-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cells"

    Article Title: Effects of Sulforaphane and 3,3?-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cells

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0086787

    Genome-wide promoter methylation profiling comparing normal prostate epithelial cells and prostate cancer cells. (A) Hierarchical clustering analysis of probes with significant scaled log 2 ratio in PrEC, LnCAP, and PC3 cells. Green and red bars represent individual probes with significant decreased and increased methylation, respectively, of MeDIP DNA samples relative to input DNA samples. Data represent the top 1,000 most significant probes within each cell line. (B) A comparison of methylation changes in LnCAP and PC3 cells relative to PrEC cells. Significant methylated probes in LnCAP and PC3 cells were compared to PrEC, and the distribution of probes with significant log2 fold-changes are shown. (C) Average methylation level in individual genes in LnCAP and PC3 cells compared to PrEC. Log2 fold-change per gene was determined by averaging the log2 fold-change of all differentially methylated probes assigned to each gene, and represented as box and whisker plots. Number above the bar denotes the number of genes in each group. Whiskers represent maximum and minimum values, and “+” represents mean value.
    Figure Legend Snippet: Genome-wide promoter methylation profiling comparing normal prostate epithelial cells and prostate cancer cells. (A) Hierarchical clustering analysis of probes with significant scaled log 2 ratio in PrEC, LnCAP, and PC3 cells. Green and red bars represent individual probes with significant decreased and increased methylation, respectively, of MeDIP DNA samples relative to input DNA samples. Data represent the top 1,000 most significant probes within each cell line. (B) A comparison of methylation changes in LnCAP and PC3 cells relative to PrEC cells. Significant methylated probes in LnCAP and PC3 cells were compared to PrEC, and the distribution of probes with significant log2 fold-changes are shown. (C) Average methylation level in individual genes in LnCAP and PC3 cells compared to PrEC. Log2 fold-change per gene was determined by averaging the log2 fold-change of all differentially methylated probes assigned to each gene, and represented as box and whisker plots. Number above the bar denotes the number of genes in each group. Whiskers represent maximum and minimum values, and “+” represents mean value.

    Techniques Used: Genome Wide, Methylation, Methylated DNA Immunoprecipitation, Whisker Assay

    5) Product Images from "Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation"

    Article Title: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

    Journal: Genome Research

    doi: 10.1101/gr.110601.110

    ( A ) Schematic showing the capture of methylated DNA into populations of single-stranded (MeDIP) or double-stranded (MBDCap) fragments. ( B ) Summarized probe intensities for enrichment of fully methylated DNA with MeDIP and two variations of MethylMiner-based
    Figure Legend Snippet: ( A ) Schematic showing the capture of methylated DNA into populations of single-stranded (MeDIP) or double-stranded (MBDCap) fragments. ( B ) Summarized probe intensities for enrichment of fully methylated DNA with MeDIP and two variations of MethylMiner-based

    Techniques Used: Methylation, Methylated DNA Immunoprecipitation

    6) Product Images from "Developmental features of DNA methylation during activation of the embryonic zebrafish genome"

    Article Title: Developmental features of DNA methylation during activation of the embryonic zebrafish genome

    Journal: Genome Biology

    doi: 10.1186/gb-2012-13-7-r65

    Promoter DNA methylation states during the transition through the MBT period . (a) MeDIP-chip profiles of DNA methylation in tiled regions spanning a housekeeping gene ( bact1 ) and developmentally regulated genes ( klf4 , pou5f1 , fez1 ) (log2 MeDIP/input ratios), in pre-MBT, MBT, and post-MBT embryos and in the ZF4 fibroblast cell line. Red arrows in the upper track point to regions analyzed by bisulfite sequencing in (b). (b) Two-dimensional scatter plots of MaxSixty values for MeDIP log 2 signal intensities at indicated developmental stages (pairwise) and in ZF4 cells. Average MaxSixty values for both MeDIP replicates are plotted for each stage. Data points are colored to indicate classification according to peak calling algorithm, to show methylated promoters in one only (purple, green) or both (blue) stages. (c) Bisulfite sequencing validation of MeDIP-chip data shown in (a); 5' to 3' orientation; filled circles indicate methylated cytosine; empty circles indicate unmethylated cytosine. (d) Numbers of methylated genes pre-MBT, MBT and post-MBT. Color reflects genes whose methylation is maintained between stages.
    Figure Legend Snippet: Promoter DNA methylation states during the transition through the MBT period . (a) MeDIP-chip profiles of DNA methylation in tiled regions spanning a housekeeping gene ( bact1 ) and developmentally regulated genes ( klf4 , pou5f1 , fez1 ) (log2 MeDIP/input ratios), in pre-MBT, MBT, and post-MBT embryos and in the ZF4 fibroblast cell line. Red arrows in the upper track point to regions analyzed by bisulfite sequencing in (b). (b) Two-dimensional scatter plots of MaxSixty values for MeDIP log 2 signal intensities at indicated developmental stages (pairwise) and in ZF4 cells. Average MaxSixty values for both MeDIP replicates are plotted for each stage. Data points are colored to indicate classification according to peak calling algorithm, to show methylated promoters in one only (purple, green) or both (blue) stages. (c) Bisulfite sequencing validation of MeDIP-chip data shown in (a); 5' to 3' orientation; filled circles indicate methylated cytosine; empty circles indicate unmethylated cytosine. (d) Numbers of methylated genes pre-MBT, MBT and post-MBT. Color reflects genes whose methylation is maintained between stages.

    Techniques Used: DNA Methylation Assay, Methylated DNA Immunoprecipitation, Chromatin Immunoprecipitation, Methylation Sequencing, Methylation

    7) Product Images from "Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells"

    Article Title: Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

    Journal: Oncotarget

    doi:

    MeDIP-chip analysis of the promoter DNA-methylome of human HEPs, HSCs and LSECs A. Two-dimensional scatter plots of MaxTen values of methylation intensities for all promoters in HEPs, HSCs and LSECs. Genes with a promoter significantly methylated in one cell type are colored; non-significantly methylated genes are shown in gray. B. Browser view of promoter methylation on all chromosomes; right , zoom-in of GFRA3 methylation in HEPs, HSCs and LSECs (log (MeDIP/Input) ratios). Red and blue colors point to methylation peaks and depletions, respectively. C. Venn diagram analysis of numbers of genes with a methylated promoter in HSCs, LSECs and HEPs. D. Most significant GO terms for the methylation ‘core’ and for cell type-specific methylated genes. E. Proportion of genes that are uniquely or commonly methylated between two or more cell types. F. Promoter methylation in HSCs, LSECs and HEPs relative to CD34 + bone marrow progenitors. Percentage of methylated genes in cell types shown on the x-axis that are also methylated in cell types shown on the y-axis.
    Figure Legend Snippet: MeDIP-chip analysis of the promoter DNA-methylome of human HEPs, HSCs and LSECs A. Two-dimensional scatter plots of MaxTen values of methylation intensities for all promoters in HEPs, HSCs and LSECs. Genes with a promoter significantly methylated in one cell type are colored; non-significantly methylated genes are shown in gray. B. Browser view of promoter methylation on all chromosomes; right , zoom-in of GFRA3 methylation in HEPs, HSCs and LSECs (log (MeDIP/Input) ratios). Red and blue colors point to methylation peaks and depletions, respectively. C. Venn diagram analysis of numbers of genes with a methylated promoter in HSCs, LSECs and HEPs. D. Most significant GO terms for the methylation ‘core’ and for cell type-specific methylated genes. E. Proportion of genes that are uniquely or commonly methylated between two or more cell types. F. Promoter methylation in HSCs, LSECs and HEPs relative to CD34 + bone marrow progenitors. Percentage of methylated genes in cell types shown on the x-axis that are also methylated in cell types shown on the y-axis.

    Techniques Used: Methylated DNA Immunoprecipitation, Chromatin Immunoprecipitation, Methylation

    Culture-induced HSC activation reprograms promoter DNA methylation A. Venn diagram analysis of the number of genes with a methylated promoter in qHSCs and aHSCs. B. Browser views of promoter methylation profiles (log (MeDIP/Input) ratios) for indicated genes in qHSCs and aHSCs. Red and blue colors point to methylation peaks and depletions, respectively. C. Heatmap of genes up-regulated and hypo-methylated after HSC activation. D. Boxwhisker plot of ACTG2 expression in qHSCs and aHSCs. E. Bisulfite sequencing analysis of CpG methylation in the ACTG2 promoter in qHSCs and aHSCs. Four CpGs are examined (columns) in 5 sequenced clones (rows). ● methylated CpG; ○ unmethylated CpG. F. Heatmap of genes down-regulated and hyper-methylated after HSC activation. G. Boxwhisker plot of APOB expression in qHSCs and aHSCs. H. Bisulfite sequencing analysis of CpG methylation in the APOB promoter in qHSCs and aHSCs. Five CpGs were analyzed.
    Figure Legend Snippet: Culture-induced HSC activation reprograms promoter DNA methylation A. Venn diagram analysis of the number of genes with a methylated promoter in qHSCs and aHSCs. B. Browser views of promoter methylation profiles (log (MeDIP/Input) ratios) for indicated genes in qHSCs and aHSCs. Red and blue colors point to methylation peaks and depletions, respectively. C. Heatmap of genes up-regulated and hypo-methylated after HSC activation. D. Boxwhisker plot of ACTG2 expression in qHSCs and aHSCs. E. Bisulfite sequencing analysis of CpG methylation in the ACTG2 promoter in qHSCs and aHSCs. Four CpGs are examined (columns) in 5 sequenced clones (rows). ● methylated CpG; ○ unmethylated CpG. F. Heatmap of genes down-regulated and hyper-methylated after HSC activation. G. Boxwhisker plot of APOB expression in qHSCs and aHSCs. H. Bisulfite sequencing analysis of CpG methylation in the APOB promoter in qHSCs and aHSCs. Five CpGs were analyzed.

    Techniques Used: Activation Assay, DNA Methylation Assay, Methylation, Methylated DNA Immunoprecipitation, Expressing, Methylation Sequencing, CpG Methylation Assay

    8) Product Images from "Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus"

    Article Title: Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1000909

    Establishment of Chromatin immunoprecipitation. (A) Nuclear localization of MoCRZ1 was visualized in the eGFP tagged strain under the native promoter. FK506 blocks nuclear localization of MoCRZ1::eGFP. Bar indicates 10 µm. (B) ChIP-chip experimental design to identify MoCRZ1 targets activated by calcium treatment. The Ca 2+ /FK506 treated sample served as the negative control treatment. (C) RT-PCR to verify that PMC1 was up-regulated in the Ca 2+ treated but not in Ca 2+ /FK506 treated sample. (D) Quantitative PCR was conducted with DNA after ChIP with antiGFP antibody. 30% input DNA collected prior to pull down was used as control. 1 µl each of ChIPed and input DNA was used for real-time PCR. Fold changes were calculated by 2 ΔΔCt , where ΔΔCt = (Ct input DNA -Ct ChIPed DNA ) Ca2+ treated sample - (Ct input DNA -Ct ChIPed DNA ) Ca2+/FK506 treated sample .
    Figure Legend Snippet: Establishment of Chromatin immunoprecipitation. (A) Nuclear localization of MoCRZ1 was visualized in the eGFP tagged strain under the native promoter. FK506 blocks nuclear localization of MoCRZ1::eGFP. Bar indicates 10 µm. (B) ChIP-chip experimental design to identify MoCRZ1 targets activated by calcium treatment. The Ca 2+ /FK506 treated sample served as the negative control treatment. (C) RT-PCR to verify that PMC1 was up-regulated in the Ca 2+ treated but not in Ca 2+ /FK506 treated sample. (D) Quantitative PCR was conducted with DNA after ChIP with antiGFP antibody. 30% input DNA collected prior to pull down was used as control. 1 µl each of ChIPed and input DNA was used for real-time PCR. Fold changes were calculated by 2 ΔΔCt , where ΔΔCt = (Ct input DNA -Ct ChIPed DNA ) Ca2+ treated sample - (Ct input DNA -Ct ChIPed DNA ) Ca2+/FK506 treated sample .

    Techniques Used: Chromatin Immunoprecipitation, Negative Control, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    9) Product Images from "Induction of altered epigenetic regulation of the hepatic glucocorticoid receptor in the offspring of rats fed a protein-restricted diet during pregnancy suggests that reduced DNA methyltransferase-1 expression is involved in impaired DNA methylation and changes in histone modifications"

    Article Title: Induction of altered epigenetic regulation of the hepatic glucocorticoid receptor in the offspring of rats fed a protein-restricted diet during pregnancy suggests that reduced DNA methyltransferase-1 expression is involved in impaired DNA methylation and changes in histone modifications

    Journal:

    doi: 10.1017/S000711450769196X

    mRNA expression of DNA methyltransferases (Dnmt (s)) in liver from 34 day-old offspring of rats fed either a control or protein-restricted (PR), or the PR diet supplemented with folic acid (PRF) diet during pregnancy. Data from RT PCR analysis are mean
    Figure Legend Snippet: mRNA expression of DNA methyltransferases (Dnmt (s)) in liver from 34 day-old offspring of rats fed either a control or protein-restricted (PR), or the PR diet supplemented with folic acid (PRF) diet during pregnancy. Data from RT PCR analysis are mean

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction

    10) Product Images from "Histone methylation levels correlate with TGFBIp and extracellular matrix gene expression in normal and granular corneal dystrophy type 2 corneal fibroblasts"

    Article Title: Histone methylation levels correlate with TGFBIp and extracellular matrix gene expression in normal and granular corneal dystrophy type 2 corneal fibroblasts

    Journal: BMC Medical Genomics

    doi: 10.1186/s12920-015-0151-8

    TGFβ1 increased H3K4me1/3 levels on TGFBIp and ECM-associated gene promoters in wild-type and GCD2-homozygous cells. a , b Bar graphs showing H3K4me3 ( a ) and H3K4me1 ( b ) levels at the indicated gene promoters in control and TGFβ1 (5 ng/ml)-stimulated wild-type and GCD2-homozygous corneal fibroblasts. ChIP assays were performed with H3K4me3 and H3K4me1 antibodies. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the indicated gene promoters to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are shown as the mean fold change of the input ± standard error (SE) of enrichment. (mean ± SE; ** P
    Figure Legend Snippet: TGFβ1 increased H3K4me1/3 levels on TGFBIp and ECM-associated gene promoters in wild-type and GCD2-homozygous cells. a , b Bar graphs showing H3K4me3 ( a ) and H3K4me1 ( b ) levels at the indicated gene promoters in control and TGFβ1 (5 ng/ml)-stimulated wild-type and GCD2-homozygous corneal fibroblasts. ChIP assays were performed with H3K4me3 and H3K4me1 antibodies. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the indicated gene promoters to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are shown as the mean fold change of the input ± standard error (SE) of enrichment. (mean ± SE; ** P

    Techniques Used: Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction

    MLL1 knockdown attenuated TGFβ1-induced increases in H3K4me3 on the promoters of TGFBIp and ECM-associated genes. a Wild-type and GCD2-homozygous corneal fibroblasts were infected with MLL1 or control shRNA lentivirus. After puromycin selection, infected cells were stimulated with TGF-β1 (5 ng/ml) for 8 h, and H3K4me3 levels at the indicated gene promoters were analyzed. ChIP assays were performed with H3K4me3 antibody. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the indicated gene promoters to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are presented as mean fold change of the input ± standard error (SE) of enrichment. (mean ± SE; ** P
    Figure Legend Snippet: MLL1 knockdown attenuated TGFβ1-induced increases in H3K4me3 on the promoters of TGFBIp and ECM-associated genes. a Wild-type and GCD2-homozygous corneal fibroblasts were infected with MLL1 or control shRNA lentivirus. After puromycin selection, infected cells were stimulated with TGF-β1 (5 ng/ml) for 8 h, and H3K4me3 levels at the indicated gene promoters were analyzed. ChIP assays were performed with H3K4me3 antibody. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the indicated gene promoters to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are presented as mean fold change of the input ± standard error (SE) of enrichment. (mean ± SE; ** P

    Techniques Used: Infection, shRNA, Selection, Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction

    TGFBIp transcription and H3K4me3 levels in wild-type and GCD2-homozygous corneal fibroblasts. a , b Slit-lamp photographs and pedigree of wild-type, GCD2 heterozygous, and GCD2 homozygous cells. c , d The mRNA and protein levels of TGFBIp in normal and GCD2 corneal fibroblasts was determined by RT-qPCR ( c ) and western blot ( d ). Gene expression was normalized to internal control GAPDH gene, and results are expressed as fold stimulation over control. e , f H3K4me3 and H3K27me3 levels at the Smad binding elements on TGFBIp gene promoters and at the TSS of TGFBIp gene in wild-type and GCD2-homozygous corneal fibroblasts. ChIP assays were performed with H3K4me3 and H3K27me3 antibodies. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the TGFBIp gene promoter to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are the mean fold change relative to the input ± standard error (SE) of enrichment. (mean ± SE; ** P
    Figure Legend Snippet: TGFBIp transcription and H3K4me3 levels in wild-type and GCD2-homozygous corneal fibroblasts. a , b Slit-lamp photographs and pedigree of wild-type, GCD2 heterozygous, and GCD2 homozygous cells. c , d The mRNA and protein levels of TGFBIp in normal and GCD2 corneal fibroblasts was determined by RT-qPCR ( c ) and western blot ( d ). Gene expression was normalized to internal control GAPDH gene, and results are expressed as fold stimulation over control. e , f H3K4me3 and H3K27me3 levels at the Smad binding elements on TGFBIp gene promoters and at the TSS of TGFBIp gene in wild-type and GCD2-homozygous corneal fibroblasts. ChIP assays were performed with H3K4me3 and H3K27me3 antibodies. Immunoprecipitated DNA and input DNA were subjected to qPCR with primers specific for the TGFBIp gene promoter to measure enrichment levels. qPCR data were analyzed using the 2 -ΔΔCt method, and data are the mean fold change relative to the input ± standard error (SE) of enrichment. (mean ± SE; ** P

    Techniques Used: Quantitative RT-PCR, Western Blot, Expressing, Binding Assay, Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction

    11) Product Images from "Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin"

    Article Title: Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1007377

    Physical association of the putative helicase (K2ORF4p), mRNA capping enzyme (K2ORF3p), and the large RNAP subunit (K2ORF6p) of the yeast VLEs with VLE-specific DNA. (A) Western blot of HA-K2ORF4p that was affinity-purified from lysates of IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. The strains used are indicated above the lanes. The antibody used is indicated on the left hand side of the strip. The protein detected is indicated on the right hand side of the strip. (B) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K1ORF3 , K2ORF3 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. Samples of individually performed gene-specific PCRs were analysed in 2.5% agarose gel stained with ethidium bromide. The identity of the bands (genes) is indicated on the right. M, DNA molecular mass marker (GeneRuler 100 bp Plus DNA Ladder, Fermentas). The respective values are indicated on the left. (C) Western blot of K2ORF3p-HA that was affinity-purified from lysates of IFO1267_pRKL2-14 (K2ORF3p-HA) and IFO1267 (control) cells. (D) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-14 and IFO1267 cells. (E) Western blot of yEGFP3-K2ORF6p that was affinity-purified from lysates of IFO1267_pRKL2-4 (yEGFP3-K2ORF6p) and IFO1267 (control) cells. (F) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using GFP-Trap agarose beads from IFO1267_pRKL2-4 and IFO1267 cells.
    Figure Legend Snippet: Physical association of the putative helicase (K2ORF4p), mRNA capping enzyme (K2ORF3p), and the large RNAP subunit (K2ORF6p) of the yeast VLEs with VLE-specific DNA. (A) Western blot of HA-K2ORF4p that was affinity-purified from lysates of IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. The strains used are indicated above the lanes. The antibody used is indicated on the left hand side of the strip. The protein detected is indicated on the right hand side of the strip. (B) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K1ORF3 , K2ORF3 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. Samples of individually performed gene-specific PCRs were analysed in 2.5% agarose gel stained with ethidium bromide. The identity of the bands (genes) is indicated on the right. M, DNA molecular mass marker (GeneRuler 100 bp Plus DNA Ladder, Fermentas). The respective values are indicated on the left. (C) Western blot of K2ORF3p-HA that was affinity-purified from lysates of IFO1267_pRKL2-14 (K2ORF3p-HA) and IFO1267 (control) cells. (D) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-14 and IFO1267 cells. (E) Western blot of yEGFP3-K2ORF6p that was affinity-purified from lysates of IFO1267_pRKL2-4 (yEGFP3-K2ORF6p) and IFO1267 (control) cells. (F) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using GFP-Trap agarose beads from IFO1267_pRKL2-4 and IFO1267 cells.

    Techniques Used: Western Blot, Affinity Purification, Stripping Membranes, Polymerase Chain Reaction, Activated Clotting Time Assay, Immunoprecipitation, Agarose Gel Electrophoresis, Staining, Marker

    12) Product Images from "Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin"

    Article Title: Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1007377

    Physical association of the putative helicase (K2ORF4p), mRNA capping enzyme (K2ORF3p), and the large RNAP subunit (K2ORF6p) of the yeast VLEs with VLE-specific DNA. (A) Western blot of HA-K2ORF4p that was affinity-purified from lysates of IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. The strains used are indicated above the lanes. The antibody used is indicated on the left hand side of the strip. The protein detected is indicated on the right hand side of the strip. (B) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K1ORF3 , K2ORF3 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. Samples of individually performed gene-specific PCRs were analysed in 2.5% agarose gel stained with ethidium bromide. The identity of the bands (genes) is indicated on the right. M, DNA molecular mass marker (GeneRuler 100 bp Plus DNA Ladder, Fermentas). The respective values are indicated on the left. (C) Western blot of K2ORF3p-HA that was affinity-purified from lysates of IFO1267_pRKL2-14 (K2ORF3p-HA) and IFO1267 (control) cells. (D) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-14 and IFO1267 cells. (E) Western blot of yEGFP3-K2ORF6p that was affinity-purified from lysates of IFO1267_pRKL2-4 (yEGFP3-K2ORF6p) and IFO1267 (control) cells. (F) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using GFP-Trap agarose beads from IFO1267_pRKL2-4 and IFO1267 cells.
    Figure Legend Snippet: Physical association of the putative helicase (K2ORF4p), mRNA capping enzyme (K2ORF3p), and the large RNAP subunit (K2ORF6p) of the yeast VLEs with VLE-specific DNA. (A) Western blot of HA-K2ORF4p that was affinity-purified from lysates of IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. The strains used are indicated above the lanes. The antibody used is indicated on the left hand side of the strip. The protein detected is indicated on the right hand side of the strip. (B) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K1ORF3 , K2ORF3 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-13 (HA-K2ORF4p) and IFO1267 (control) cells. Samples of individually performed gene-specific PCRs were analysed in 2.5% agarose gel stained with ethidium bromide. The identity of the bands (genes) is indicated on the right. M, DNA molecular mass marker (GeneRuler 100 bp Plus DNA Ladder, Fermentas). The respective values are indicated on the left. (C) Western blot of K2ORF3p-HA that was affinity-purified from lysates of IFO1267_pRKL2-14 (K2ORF3p-HA) and IFO1267 (control) cells. (D) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using anti-HA HA-7 agarose from IFO1267_pRKL2-14 and IFO1267 cells. (E) Western blot of yEGFP3-K2ORF6p that was affinity-purified from lysates of IFO1267_pRKL2-4 (yEGFP3-K2ORF6p) and IFO1267 (control) cells. (F) PCR analysis of the presence of chromosomal ( ACT , HGT1 ) or VLE ( K2ORF3 , K2ORF6 ) DNA in chromatin immunoprecipitated using GFP-Trap agarose beads from IFO1267_pRKL2-4 and IFO1267 cells.

    Techniques Used: Western Blot, Affinity Purification, Stripping Membranes, Polymerase Chain Reaction, Activated Clotting Time Assay, Immunoprecipitation, Agarose Gel Electrophoresis, Staining, Marker

    13) Product Images from "Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes"

    Article Title: Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes

    Journal: Nature Communications

    doi: 10.1038/ncomms3889

    Folate deficiency alters sperm DNA methylation. Changes in DNA methylation are illustrated by smoothed MeDIP over input log2 ratios of individual oligonucleotides for the folate-sufficient (FS) and the folate-deficient (FD) animals. The gene is indicated at the bottom of the graph and the arrow represents the transcription start site (TSS).
    Figure Legend Snippet: Folate deficiency alters sperm DNA methylation. Changes in DNA methylation are illustrated by smoothed MeDIP over input log2 ratios of individual oligonucleotides for the folate-sufficient (FS) and the folate-deficient (FD) animals. The gene is indicated at the bottom of the graph and the arrow represents the transcription start site (TSS).

    Techniques Used: DNA Methylation Assay, Methylated DNA Immunoprecipitation

    Folate deficiency alters sperm DNA methylation at genes implicated in development and metabolic processes. Sequenom MassARRAY methylation analysis was performed on selected targets of interest identified by MeDIP-chip as altered in FD versus FS sperm. FD sperm had significantly reduced 5-methylcytosine at CpG locations of Rfwd2 ( a ), Sfi1 ( b ), Kdm3b ( c ) , Gm52 ( d ) and Rbks ( e ). Means±s.e.m. of five determinations are shown. * P
    Figure Legend Snippet: Folate deficiency alters sperm DNA methylation at genes implicated in development and metabolic processes. Sequenom MassARRAY methylation analysis was performed on selected targets of interest identified by MeDIP-chip as altered in FD versus FS sperm. FD sperm had significantly reduced 5-methylcytosine at CpG locations of Rfwd2 ( a ), Sfi1 ( b ), Kdm3b ( c ) , Gm52 ( d ) and Rbks ( e ). Means±s.e.m. of five determinations are shown. * P

    Techniques Used: DNA Methylation Assay, Methylation, Methylated DNA Immunoprecipitation, Chromatin Immunoprecipitation

    14) Product Images from "Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice"

    Article Title: Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0018216

    Overview of study design and data integration. ( A ) Experimental strategy for the identification and integration of PB-induced expression and epigenetic perturbations in target (liver) and non-target (kidney) tissues. RNA, DNA and chromatin was extracted from liver and kidney samples of control and PB-treated (4-week, 0.05% in drinking water) B6C3F1 male mice (n = 10 per group) and analyzed through the different profiling methodologies and platforms indicated. Abbreviations: liquid chromatography-mass spectrometry (LC-MS), Methylated DNA immunoprecipitation (MeDIP), Chromatin immunoprecipitation (ChIP), quantitative real-time PCR (qPCR). ( B ) Summary of bioinformatic data integration strategy. For each annotated gene present on gene expression and promoter arrays, the expression and DNA methylation values were mapped to the genome and correlated to examine the functional links between expression and methylation levels at individual loci upon phenobarbital treatment. For loci of interest the abundance of selected chromatin marks were quantified. Coverage of the promoter array (1.8 kb per promoter: 500 bp downstream and 1300 bp upstream of the transcriptional start site (TSS)) is shown. For the methylation analysis a window of 100 bp downstream and 800 bp upstream of the TSS was used. The figure shows an exemplary gene that upon treatment loses DNA methylation and gets expressed.
    Figure Legend Snippet: Overview of study design and data integration. ( A ) Experimental strategy for the identification and integration of PB-induced expression and epigenetic perturbations in target (liver) and non-target (kidney) tissues. RNA, DNA and chromatin was extracted from liver and kidney samples of control and PB-treated (4-week, 0.05% in drinking water) B6C3F1 male mice (n = 10 per group) and analyzed through the different profiling methodologies and platforms indicated. Abbreviations: liquid chromatography-mass spectrometry (LC-MS), Methylated DNA immunoprecipitation (MeDIP), Chromatin immunoprecipitation (ChIP), quantitative real-time PCR (qPCR). ( B ) Summary of bioinformatic data integration strategy. For each annotated gene present on gene expression and promoter arrays, the expression and DNA methylation values were mapped to the genome and correlated to examine the functional links between expression and methylation levels at individual loci upon phenobarbital treatment. For loci of interest the abundance of selected chromatin marks were quantified. Coverage of the promoter array (1.8 kb per promoter: 500 bp downstream and 1300 bp upstream of the transcriptional start site (TSS)) is shown. For the methylation analysis a window of 100 bp downstream and 800 bp upstream of the TSS was used. The figure shows an exemplary gene that upon treatment loses DNA methylation and gets expressed.

    Techniques Used: Expressing, Mouse Assay, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy, Methylation, Immunoprecipitation, Methylated DNA Immunoprecipitation, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, DNA Methylation Assay, Functional Assay

    MeDIP-promoter array profiling of the methylome in the liver of control and PB treated B6C3F1 mice. ( A ) An antibody directed against 5-methyl-cytosine (5mC) was used for immunoprecipitation of methylated DNA. Control sequences that are highly methylated (IAP, H19 ICR) or lack CpGs (CSa) were selected as controls for the MeDIP experiment prior to and following whole genome amplification (WGA). The relative enrichment in the bound over input fractions for 10 individual biological replicates was measured by qPCR. ( B ) Methylation comparison between liver of control and PB-treated mice (average log 2 (IP/total) for replicates) in all 23,428 Nimblegen probe sets. The colors indicate the CpG island class for those probe sets where the log 2 methylation ratio of PB-treated vs. control (difference in M-value) is significant (p≤0.01 and an absolute log 2 fold change of ≥0.2, 28 probe sets), non-differentially methylated regions are indicated in grey. A circle highlights Cyp2b10 .
    Figure Legend Snippet: MeDIP-promoter array profiling of the methylome in the liver of control and PB treated B6C3F1 mice. ( A ) An antibody directed against 5-methyl-cytosine (5mC) was used for immunoprecipitation of methylated DNA. Control sequences that are highly methylated (IAP, H19 ICR) or lack CpGs (CSa) were selected as controls for the MeDIP experiment prior to and following whole genome amplification (WGA). The relative enrichment in the bound over input fractions for 10 individual biological replicates was measured by qPCR. ( B ) Methylation comparison between liver of control and PB-treated mice (average log 2 (IP/total) for replicates) in all 23,428 Nimblegen probe sets. The colors indicate the CpG island class for those probe sets where the log 2 methylation ratio of PB-treated vs. control (difference in M-value) is significant (p≤0.01 and an absolute log 2 fold change of ≥0.2, 28 probe sets), non-differentially methylated regions are indicated in grey. A circle highlights Cyp2b10 .

    Techniques Used: Methylated DNA Immunoprecipitation, Mouse Assay, Immunoprecipitation, Methylation, Whole Genome Amplification, Real-time Polymerase Chain Reaction

    Cyp2b10 is selectively DNA demethylated and over expressed in the liver of PB-treated B6C3F1 mice. ( A ) RT-qPCR analysis of Cy2b10 expression in the liver and the kidney of control and PB-treated animals. Fold changes are indicated relative to 18S RNA expression levels. ( B ) MeDIP-qPCR validation of Nimblegen data. Positive (H19 ICR, IAP), negative (CSa, Intergenic3, Hprt, Gapdh) and selected regions identified on the promoter array were assessed by qPCR from WGA amplified MeDIP and input DNA samples prepared from the liver of 6 control and PB-treated mice. qPCR identified selective demethylation at Cyp2b10 TSS, both in the promoter and first intron (location of PCR amplicons is shown in Figure 3C). Relative enrichment (IP/Input) for DNA methylation of 6 individual biological replicates is shown. ( C ) Bisulfite sequencing at Cyp2b10 first intron. Sequenced area is shown by the two arrows in the schematic gene map. Each line represents the sequence of a single clone. CpGs are shown as white (unmethylated) or black (methylated) circles. The values above summarizes the overall methylation level of this region (percentage of methylated CpG in all sequenced clones) ( D ) Quantitative DNA methylation analysis by pyrosequencing of two Cyp2b10 promoter CpG sites (CpG1: -914 and CpG2: -886 indicated in (C)) in the liver and kidney of control and PB-treated animals. Standard deviation was calculated from 10 biological replicates. Primers/genomic regions used for bisulfite sequencing are available in Figure S9.
    Figure Legend Snippet: Cyp2b10 is selectively DNA demethylated and over expressed in the liver of PB-treated B6C3F1 mice. ( A ) RT-qPCR analysis of Cy2b10 expression in the liver and the kidney of control and PB-treated animals. Fold changes are indicated relative to 18S RNA expression levels. ( B ) MeDIP-qPCR validation of Nimblegen data. Positive (H19 ICR, IAP), negative (CSa, Intergenic3, Hprt, Gapdh) and selected regions identified on the promoter array were assessed by qPCR from WGA amplified MeDIP and input DNA samples prepared from the liver of 6 control and PB-treated mice. qPCR identified selective demethylation at Cyp2b10 TSS, both in the promoter and first intron (location of PCR amplicons is shown in Figure 3C). Relative enrichment (IP/Input) for DNA methylation of 6 individual biological replicates is shown. ( C ) Bisulfite sequencing at Cyp2b10 first intron. Sequenced area is shown by the two arrows in the schematic gene map. Each line represents the sequence of a single clone. CpGs are shown as white (unmethylated) or black (methylated) circles. The values above summarizes the overall methylation level of this region (percentage of methylated CpG in all sequenced clones) ( D ) Quantitative DNA methylation analysis by pyrosequencing of two Cyp2b10 promoter CpG sites (CpG1: -914 and CpG2: -886 indicated in (C)) in the liver and kidney of control and PB-treated animals. Standard deviation was calculated from 10 biological replicates. Primers/genomic regions used for bisulfite sequencing are available in Figure S9.

    Techniques Used: Mouse Assay, Quantitative RT-PCR, Expressing, RNA Expression, Methylated DNA Immunoprecipitation, Real-time Polymerase Chain Reaction, Whole Genome Amplification, Amplification, Polymerase Chain Reaction, DNA Methylation Assay, Methylation Sequencing, Sequencing, Methylation, Standard Deviation

    15) Product Images from "Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome"

    Article Title: Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

    Journal: Clinical Epigenetics

    doi: 10.1186/s13148-016-0181-x

    FMR1 locus (h)MeDIP profiling identifies novel regions of 5mC and 5hmC changes in FXS patient PBMC samples. a . Experimental overview. Methylated DNA immunoprecipitation (MeDIP) assay was used to profile DNA methylation (5mC), DNA hydroxymethylation (5hmC). Chromatin immunoprecipitation (ChIP) was used to profile histone post-translational modifications (PTM). Antibody (Ab) b – c . The graphs illustrate the relative enrichment of the indicated mark (log2 fold enrichment) in FXS ( red ) and control ( blue ) PBMCs. The upper panel illustrates the chromosomal and genomic location locations as well as the indicated referenced Refseq genes: FMR1 , and referenced antisense non coding RNAs ( FMR1AS1 and L29074.3). This snapshot illustrates the epigenetic landscape over a region covering 79 kb on ChrX: 146971000-147050000 ( c ). RPL19 and GAPDH provide controls regions of no changes in 5mC and 5hmC ( b ). In the graphs, the thicker lines indicate higher deviation between biological replicates (controls n = 4; FXS n = 8) (aggregation mean, sliding window 529 bp). Regions I to V were selected as regions of strongest apparent epigenetic variation across epigenetic marks and cell types based on epigenomic landscape visualization illustrated in Figs. 1 and 3 . The chromosome coordinates of these regions are provided in Table 1
    Figure Legend Snippet: FMR1 locus (h)MeDIP profiling identifies novel regions of 5mC and 5hmC changes in FXS patient PBMC samples. a . Experimental overview. Methylated DNA immunoprecipitation (MeDIP) assay was used to profile DNA methylation (5mC), DNA hydroxymethylation (5hmC). Chromatin immunoprecipitation (ChIP) was used to profile histone post-translational modifications (PTM). Antibody (Ab) b – c . The graphs illustrate the relative enrichment of the indicated mark (log2 fold enrichment) in FXS ( red ) and control ( blue ) PBMCs. The upper panel illustrates the chromosomal and genomic location locations as well as the indicated referenced Refseq genes: FMR1 , and referenced antisense non coding RNAs ( FMR1AS1 and L29074.3). This snapshot illustrates the epigenetic landscape over a region covering 79 kb on ChrX: 146971000-147050000 ( c ). RPL19 and GAPDH provide controls regions of no changes in 5mC and 5hmC ( b ). In the graphs, the thicker lines indicate higher deviation between biological replicates (controls n = 4; FXS n = 8) (aggregation mean, sliding window 529 bp). Regions I to V were selected as regions of strongest apparent epigenetic variation across epigenetic marks and cell types based on epigenomic landscape visualization illustrated in Figs. 1 and 3 . The chromosome coordinates of these regions are provided in Table 1

    Techniques Used: Methylation, Immunoprecipitation, Methylated DNA Immunoprecipitation, DNA Methylation Assay, Chromatin Immunoprecipitation

    16) Product Images from "Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression"

    Article Title: Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression

    Journal: Translational Psychiatry

    doi: 10.1038/tp.2016.136

    Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone H3 acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input DNA. Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P
    Figure Legend Snippet: Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone H3 acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input DNA. Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Activity Assay, Over Expression, Chromatin Immunoprecipitation

    17) Product Images from "Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii"

    Article Title: Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky373

    TgAP2X-5 depletion prevents TgAP2XI-5 binding to a number of promoters. ( A ) ChIP-on-chip data are represented as the log 2 ratio of the hybridization signal given by DNA immunoprecipitated over the signal given by the non-enriched input DNA. The log 2 ratio of each oligonucleotide present on the tiled microarray has been plotted at the respective genomic position. Genes above the horizontal axis are encoded the forward strand whereas those below are encoded the reverse strand. The scale of the Y -axis was kept identical for all representation to allow the comparison of signals. TgAP2XI-5 ChIP-chip assay is represented for the TgAP2XI-5 protein in the parental strain (RH ΔhxgprtΔku80 , green, negative control) or TgAP2XI-5 tagged strain (red, positive control) or TgAP2XI-5 tagged in the iKD TgAP2X-5 strain in presence of ATc (orange). The associated peaks identified by the mPeak algorithm are also provided. A portion of the Toxoplasma gondii chromosome III is represented. The boxed promoter presents a lower enrichment of TgAP2XI-5 in the iKD TgAP2X-5 strain in presence of ATc. ( B ) Representation of the ChIP-chip experiments for a portion of chromosome IV which encompasses the TgROP15 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( C ) Representation of the ChIP-chip experiments for a portion of chromosome III which encompasses the TgROP24 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( D ) Quantitative PCR was performed on the TgAP2XI-5 ChIP assays performed in the iKD TgAP2X-5/TgAP2XI-5 strain (orange), iKD TgAP2X-5 complemented/TgAP2XI-5 strain (yellow), TgAP2XI-5-tagged strain (red) and parental strain (negative control, green). Amplification was carried out on regions within the promoter of each of the six genes listed. The enrichment for corresponding ChIP DNA samples is presented as a percentage of INPUT for each target.
    Figure Legend Snippet: TgAP2X-5 depletion prevents TgAP2XI-5 binding to a number of promoters. ( A ) ChIP-on-chip data are represented as the log 2 ratio of the hybridization signal given by DNA immunoprecipitated over the signal given by the non-enriched input DNA. The log 2 ratio of each oligonucleotide present on the tiled microarray has been plotted at the respective genomic position. Genes above the horizontal axis are encoded the forward strand whereas those below are encoded the reverse strand. The scale of the Y -axis was kept identical for all representation to allow the comparison of signals. TgAP2XI-5 ChIP-chip assay is represented for the TgAP2XI-5 protein in the parental strain (RH ΔhxgprtΔku80 , green, negative control) or TgAP2XI-5 tagged strain (red, positive control) or TgAP2XI-5 tagged in the iKD TgAP2X-5 strain in presence of ATc (orange). The associated peaks identified by the mPeak algorithm are also provided. A portion of the Toxoplasma gondii chromosome III is represented. The boxed promoter presents a lower enrichment of TgAP2XI-5 in the iKD TgAP2X-5 strain in presence of ATc. ( B ) Representation of the ChIP-chip experiments for a portion of chromosome IV which encompasses the TgROP15 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( C ) Representation of the ChIP-chip experiments for a portion of chromosome III which encompasses the TgROP24 gene (yellow). Two repeats (R1 and R2) are presented for each ChIP experiment along with the mPeak identified peaks. ( D ) Quantitative PCR was performed on the TgAP2XI-5 ChIP assays performed in the iKD TgAP2X-5/TgAP2XI-5 strain (orange), iKD TgAP2X-5 complemented/TgAP2XI-5 strain (yellow), TgAP2XI-5-tagged strain (red) and parental strain (negative control, green). Amplification was carried out on regions within the promoter of each of the six genes listed. The enrichment for corresponding ChIP DNA samples is presented as a percentage of INPUT for each target.

    Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Hybridization, Immunoprecipitation, Microarray, Negative Control, Positive Control, Real-time Polymerase Chain Reaction, Amplification

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    Purification:

    Article Title: Cellular Uptake of Tile-Assembled DNA Nanotubes
    Article Snippet: .. Purification of the assembled DNA nanotubes was done using 30K Amicon Ultra 0.5-mL centrifuge filters (30000 MWCO, Millipore, Schwalbach, Germany) to remove excess strands that were not folded into the structures. .. One hundred microliters of assembled DNA nanotube solution were mixed with 400 µL of folding buffer, filled into the centrifuge filter, and centrifuged 3 times at 13,000× g for 6 min. After every centrifuge step, the flow-through was removed and the filter was refilled up to 500 µL with buffer.

    Article Title: Next Generation Sequencing-Based Comprehensive Chromosome Screening in Mouse Polar Bodies, Oocytes, and Embryos 1
    Article Snippet: .. WGA DNA was purified using GenElute PCR cleanup columns (Sigma-Aldrich) and quantified using a Nanodrop 8000 spectrophotometer (Fisher Scientific Inc., Waltham, MA). .. WGA DNA was normalized to 200 ng in a total volume of 35 μl of molecular biological grade water (Lonza, Rockland, ME).

    Immunoprecipitation:

    Article Title: Kaposi's Sarcoma-Associated Herpesvirus Lytic Switch Protein Stimulates DNA Binding of RBP-Jk/CSL To Activate the Notch Pathway
    Article Snippet: .. For BCBL-1, 293, BL-41, or BJAB cells, protein-DNA complexes were immunoprecipitated as described above or with anti-VP16 antibody (Sigma). .. Immunoprecipitated complexes were collected with 60 μl of 50% (vol/vol) protein A agarose for 2 h at 4°C.

    Polymerase Chain Reaction:

    Article Title: Next Generation Sequencing-Based Comprehensive Chromosome Screening in Mouse Polar Bodies, Oocytes, and Embryos 1
    Article Snippet: .. WGA DNA was purified using GenElute PCR cleanup columns (Sigma-Aldrich) and quantified using a Nanodrop 8000 spectrophotometer (Fisher Scientific Inc., Waltham, MA). .. WGA DNA was normalized to 200 ng in a total volume of 35 μl of molecular biological grade water (Lonza, Rockland, ME).

    Injection:

    Article Title: HMGB1 Promotes Systemic Lupus Erythematosus by Enhancing Macrophage Inflammatory Response
    Article Snippet: .. To generate the murine model of SLE, six-week-old female BALB/c mice were immunized s.c. with ALD-DNA (50 μ g/mouse) plus CFA (Sigma-Aldrich) on day 1, followed by s.c. injection of ALD-DNA (50 μ g/mouse) emulsified with CFA (Sigma-Aldrich) on days 14 and 28 for total of three times as described previously [ – ]. .. Mice in each group received an equal volume of PBS plus CFA or IFA, or UnALD-DNA (50 mg/mouse) plus CFA or IFA were used as controls.

    Mouse Assay:

    Article Title: HMGB1 Promotes Systemic Lupus Erythematosus by Enhancing Macrophage Inflammatory Response
    Article Snippet: .. To generate the murine model of SLE, six-week-old female BALB/c mice were immunized s.c. with ALD-DNA (50 μ g/mouse) plus CFA (Sigma-Aldrich) on day 1, followed by s.c. injection of ALD-DNA (50 μ g/mouse) emulsified with CFA (Sigma-Aldrich) on days 14 and 28 for total of three times as described previously [ – ]. .. Mice in each group received an equal volume of PBS plus CFA or IFA, or UnALD-DNA (50 mg/mouse) plus CFA or IFA were used as controls.

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  • 99
    Millipore input dna
    Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone <t>H3</t> acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input <t>DNA.</t> Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P
    Input Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 126 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/input dna/product/Millipore
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    99
    Millipore total genomic dna input
    Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone <t>H3</t> acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input <t>DNA.</t> Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P
    Total Genomic Dna Input, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total genomic dna input/product/Millipore
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    total genomic dna input - by Bioz Stars, 2020-07
    99/100 stars
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    Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone H3 acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input DNA. Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P

    Journal: Translational Psychiatry

    Article Title: Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression

    doi: 10.1038/tp.2016.136

    Figure Lengend Snippet: Gene and miRNA expression levels were measured in the prefrontal cortex of FSL with/without access to running wheel (FSL-runners versus FSL-controls) using RT-PCR. ( a ) Physical activity normalized Il6 levels in the FSL-runner group but had no effect on Lin28b and Drosha mRNA levels. ( b ) In line with an Il6 reduction in the FSL rats that were running, let-7i and miR-98 showed significantly increased expression. Specifically, upregulation of let-7i was associated with primary let-7i overexpression ( c ). ( d ) Chromatin immunoprecipitation (ChIP) showed an increased histone H4 acetylation (H4ac) but not histone H3 acetylation (H3ac) within the pri-let-7i promoter of the FSL-runners. Gene expression data were presented as relative quantifications (R.Q.), two reference genes ( Gapdh and Ppia ) were used for normalization of Il6 , Lin28b , Drosha and the primary miRNA genes. Rnu5g was used for normalization of mature miRNAs. ChIP data are presented as percentage of genomic input DNA. Data are presented as group means±s.e.m. For all figures: n =5–7 animals per group, * P

    Article Snippet: Sonicated DNA was either aliquoted as genomic input DNA or immunoprecipitated using an anti-acetyl-histone H3 antibody (#06-599; EMD Millipore, Billerica, MA, USA), anti-acetyl-histone H4 antibody (#06-598; Millipore) or normal rabbit IgG (negative control; Millipore) at 4 °C overnight with rotation.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Activity Assay, Over Expression, Chromatin Immunoprecipitation