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  • 97
    Zymo Research bisulfite converted dna
    Phospho-Vitamin C induces demethylation of FOXP3 <t>TSDR</t> in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic <t>DNA</t> was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p
    Bisulfite Converted Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 97/100, based on 395 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore converted dna
    Phospho-Vitamin C induces demethylation of FOXP3 <t>TSDR</t> in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic <t>DNA</t> was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p
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    Millipore bisulfite converted dna
    Phospho-Vitamin C induces demethylation of FOXP3 <t>TSDR</t> in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic <t>DNA</t> was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p
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    91
    Thermo Fisher converted dna
    Phospho-Vitamin C induces demethylation of FOXP3 <t>TSDR</t> in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic <t>DNA</t> was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p
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    91
    ATUM converted dna
    Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng <t>DNA).</t> (b) The distribution of CG-DMRs (identified by comparing <t>RRBS</t> data take with C1–6 and V1–6) in various genomic features.
    Converted Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 91/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    ATUM bisulphite converted dna
    Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng <t>DNA).</t> (b) The distribution of CG-DMRs (identified by comparing <t>RRBS</t> data take with C1–6 and V1–6) in various genomic features.
    Bisulphite Converted Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    ATUM bs converted dna
    Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng <t>DNA).</t> (b) The distribution of CG-DMRs (identified by comparing <t>RRBS</t> data take with C1–6 and V1–6) in various genomic features.
    Bs Converted Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATUM bisulfite converted dna
    Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng <t>DNA).</t> (b) The distribution of CG-DMRs (identified by comparing <t>RRBS</t> data take with C1–6 and V1–6) in various genomic features.
    Bisulfite Converted Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 92/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Sequenom bisulfite converted dna
    <t>DNA</t> methylation and expressional alterations of miR-340 ( a ) Relative expression of miR-340 in SK-N-BE and SHSY-5Y at 7 days post-ATRA. ( b,c ) Kaplan Meier survival plots for OS ( b ) and EFS ( c ) in 237 neuroblastoma tumors based on miR-340 expression. ( d ) SignalMap image from <t>MeDIP</t> analysis for the miR-340 upstream region. Only the methylation peak highlighted with a bracket (~6 Kb upstream) exhibited significant de-methylation in SK-N-BE cells 7 days post-ATRA. This peak overlaps the predicted TSS for miR-340. ( e ) Scatter plot of methylation vs. miR-340 expression in tumors showing a significant inverse correlation using Pearson’s correlation coefficient. ( f ) Expression of miR-340 following 5’-Aza-2 treatment of SK-N-BE and SHSY-5Y (*P
    Bisulfite Converted Dna, supplied by Sequenom, used in various techniques. Bioz Stars score: 93/100, based on 171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc converted dna
    Overview of <t>DNA</t> methylation during thymocyte maturation. ( A ) Principal component analysis of all samples based on methylation profiles obtained from <t>HM450</t> arrays. Arrows represent the direction of differentiation. ( B ) Venn diagrams showing all annotated DMRs at each differentiation step. ( C ) Genomic distribution of the thymic DMRs at each differentiation step using CIRCOS. Colored bars represent the Δ M -value. The gray lines intersect at Δ M = 0.
    Converted Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 265 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies converted dna
    Overview of <t>DNA</t> methylation during thymocyte maturation. ( A ) Principal component analysis of all samples based on methylation profiles obtained from <t>HM450</t> arrays. Arrows represent the direction of differentiation. ( B ) Venn diagrams showing all annotated DMRs at each differentiation step. ( C ) Genomic distribution of the thymic DMRs at each differentiation step using CIRCOS. Colored bars represent the Δ M -value. The gray lines intersect at Δ M = 0.
    Converted Dna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Sequenom converted dna
    Analysis of <t>DNA</t> methylation status of miR-200f promoter sequences in breast tumors. ( A ) Schematic depiction of miR- 200b-a-429 and miR-200c-141 genomic loci showing CpG islands (green), putative transcription start sites (TSS) and miRNA stem-loop sequences (red). The regions analyzed for DNA methylation (MassArray) are indicated by a black bar. Chromosomal location is indicated between brackets. ( B ) The DNA methylation levels across the regions shown in panel ( A ) were quantified in breast cancers by <t>Sequenom</t> MassArray® MALDI-TOF platform. The mean percentage of methylation levels in three tumor types (ER+, TN, MBC) are represented as box-plots. Statistical significance was determined by Student’s t test. ( C ) Expression and %CpG methylation data are represented on a scatter plot matrix showing correlation between the indicated variables, a 95% bivariate normal density ellipse is imposed on each scatterplot. Pearson correlation coefficients (R) and significance probabilities (P) are shown. Statistically significant p values (
    Converted Dna, supplied by Sequenom, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Roche converted dna
    Analysis of <t>DNA</t> methylation status of miR-200f promoter sequences in breast tumors. ( A ) Schematic depiction of miR- 200b-a-429 and miR-200c-141 genomic loci showing CpG islands (green), putative transcription start sites (TSS) and miRNA stem-loop sequences (red). The regions analyzed for DNA methylation (MassArray) are indicated by a black bar. Chromosomal location is indicated between brackets. ( B ) The DNA methylation levels across the regions shown in panel ( A ) were quantified in breast cancers by <t>Sequenom</t> MassArray® MALDI-TOF platform. The mean percentage of methylation levels in three tumor types (ER+, TN, MBC) are represented as box-plots. Statistical significance was determined by Student’s t test. ( C ) Expression and %CpG methylation data are represented on a scatter plot matrix showing correlation between the indicated variables, a 95% bivariate normal density ellipse is imposed on each scatterplot. Pearson correlation coefficients (R) and significance probabilities (P) are shown. Statistically significant p values (
    Converted Dna, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    TaKaRa amplification converted dna
    Analysis of <t>DNA</t> methylation status of miR-200f promoter sequences in breast tumors. ( A ) Schematic depiction of miR- 200b-a-429 and miR-200c-141 genomic loci showing CpG islands (green), putative transcription start sites (TSS) and miRNA stem-loop sequences (red). The regions analyzed for DNA methylation (MassArray) are indicated by a black bar. Chromosomal location is indicated between brackets. ( B ) The DNA methylation levels across the regions shown in panel ( A ) were quantified in breast cancers by <t>Sequenom</t> MassArray® MALDI-TOF platform. The mean percentage of methylation levels in three tumor types (ER+, TN, MBC) are represented as box-plots. Statistical significance was determined by Student’s t test. ( C ) Expression and %CpG methylation data are represented on a scatter plot matrix showing correlation between the indicated variables, a 95% bivariate normal density ellipse is imposed on each scatterplot. Pearson correlation coefficients (R) and significance probabilities (P) are shown. Statistically significant p values (
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    91
    Sequenom bisulphite converted dna
    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of <t>DNA</t> (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 <t>RT-PCR</t> data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.
    Bisulphite Converted Dna, supplied by Sequenom, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen bisulfite converted epitect control dna
    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of <t>DNA</t> (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 <t>RT-PCR</t> data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.
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    93
    Illumina Inc bisulphite converted dna
    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of <t>DNA</t> (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 <t>RT-PCR</t> data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.
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    85
    EpigenDx non converted dna
    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of <t>DNA</t> (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 <t>RT-PCR</t> data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.
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    86
    Promega • converted methylated human control dna
    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of <t>DNA</t> (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 <t>RT-PCR</t> data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.
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    Image Search Results


    Phospho-Vitamin C induces demethylation of FOXP3 TSDR in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic DNA was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p

    Journal: Scientific Reports

    Article Title: Vitamin C supports conversion of human γδ T cells into FOXP3-expressing regulatory cells by epigenetic regulation

    doi: 10.1038/s41598-020-63572-w

    Figure Lengend Snippet: Phospho-Vitamin C induces demethylation of FOXP3 TSDR in TGF-β-expanded Vδ2 T cells. MACS-sorted Vδ2 T cells were activated with BrHPP or A/E-beads and expanded in complete medium supplemented with IL-2 and TGF-β and the additional presence or absence of pVC (50 µg/mL). On day eight, FOXP3 + and FOXP3 − Vδ2 T cells were sorted by FACS. Genomic DNA was isolated and subjected to pyrosequencing to determine the methylation status of TSDR. Input cells (MACS-sorted Vδ2 T cells) were included for comparison. ( a) Data from four independent experiments are depicted. Each row represents the methylation status of an individual CpG motif within the TSDR. The columns show data from independent donors under the indicated experimental conditions. The methylation rates were translated into a color code from yellow (0%) via green (50%) up to blue (100%). ( b,c) Graphs show the average methylation status of the TSDR in (b) FOXP3 + and (c) FOXP3 − Vδ2 T cells. Each symbol represents an individual donor. ** p

    Article Snippet: The human Treg-specific demethylated region (TSDR) was amplified by PCR using bisulfite-converted DNA, the primers hTSDR-for (5′GAGATGATTTGTTTGGGGGTAGAGGA-3′), hTSDR-rev (5′-bio- AACACCCATATCACCCCACCT-3′) and the ZymoTaq PreMix (Zymo Research) according to the manufacturer’s protocol.

    Techniques: Magnetic Cell Separation, FACS, Isolation, Methylation

    Analysis of NDRG2 gene promoter methylation in PA samples. a Methylation frequency (%). b Hormone distribution of PAs in methylated and unmethylated NDRG2 promoter groups. PRL – prolactin, IGF-1 – insulin-like grow factor 1, GH – growth hormone, ACTH – adrenocorticotropic hormone, multiple – PAs secreting more than one hormone, NS – non-secreting PAs. c Representative MS-PCR for NDRG2 in PA samples. M indicates amplification of methylated alleles, U unmethylated alleles. M cont. – positive methylation control (Standard Bisulfite Converted Universal Methylated Human DNA), U cont. – negative methylation control (normal human peripheral lymphocytes), H2O – water control, I-VI designate PA samples

    Journal: Diagnostic Pathology

    Article Title: N-myc downstream-regulated gene 2 (NDRG2) promoter methylation and expression in pituitary adenoma

    doi: 10.1186/s13000-017-0622-7

    Figure Lengend Snippet: Analysis of NDRG2 gene promoter methylation in PA samples. a Methylation frequency (%). b Hormone distribution of PAs in methylated and unmethylated NDRG2 promoter groups. PRL – prolactin, IGF-1 – insulin-like grow factor 1, GH – growth hormone, ACTH – adrenocorticotropic hormone, multiple – PAs secreting more than one hormone, NS – non-secreting PAs. c Representative MS-PCR for NDRG2 in PA samples. M indicates amplification of methylated alleles, U unmethylated alleles. M cont. – positive methylation control (Standard Bisulfite Converted Universal Methylated Human DNA), U cont. – negative methylation control (normal human peripheral lymphocytes), H2O – water control, I-VI designate PA samples

    Article Snippet: For each set of methylation-specific PCR reactions methylated (Bisulfite-Converted Universal Methylated Human DNA Standard (Zymo Research, USA)), unmethylated (human blood lymphocyte DNA, treated with bisulfite) and negative (nuclease-free water) controls were included in all reactions.

    Techniques: Methylation, Mass Spectrometry, Polymerase Chain Reaction, Amplification

    Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng DNA). (b) The distribution of CG-DMRs (identified by comparing RRBS data take with C1–6 and V1–6) in various genomic features.

    Journal: Nature biomedical engineering

    Article Title: Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

    doi:

    Figure Lengend Snippet: Methylomic changes in NeuN+ fraction from mouse frontal cortex associated with chronic clozapine treatment (a) Pearson’s correlations among various datasets. Each group of mice has 6 biological replicates (C1–6 for clozapine-treated mice and V1–6 for control mice injected with vehicle) and each sample had 2 technical replicates (R1 and R2, each obtained with 10 ng DNA). (b) The distribution of CG-DMRs (identified by comparing RRBS data take with C1–6 and V1–6) in various genomic features.

    Article Snippet: PCR amplification and sequencing of single-cell RRBS samples The converted DNA (20 μl) was amplified by two rounds of PCR.

    Techniques: Mouse Assay, Injection

    MID-RRBS generated high quality data using sub-1 ng DNA (a) The percentage of the theoretical maximum of CpGs covered at 1× and 10× coverage with starting DNA samples of various amounts. MspI in silico digestion followed by size selection of the hg19 genome produces the theoretical maximum of 2,782,793 CpGs. The centre represents mean. (b) Pearson’s correlations in the CG methylation level among various samples processed by MID-RRBS and Zymo kit. CpGs with ≥25× coverage were examined in the calculations. n = 14871. (c) MID-RRBS coverage of gene promoters (2 kb regions upstream of transcription starting sites of RefSeq genes), CpG islands (UCSC annotation database), CpG island shores (2 kb regions adjacent to CpG islands), enhancers (regions defined by H3K4me1+ H3K27ac based on ENCODE ChIP-seq data of GM12878 cells, ENCFF001SUE and ENCFF660QDF), and 5 kb tiles (non-overlapping consecutive 5 kb windows), in comparison to those of 1 μg and 1 ng samples processed by the Zymo kit. (d) The number of CpGs with various coverages (0–100×), in comparison to those of data produced using Zymo kit, mRRBS 30 , and LCM-RRBS 34 . (e) Saturation analysis of MID-RRBS data in comparison with other works. The analysis was conducted by random selection of a number of raw reads followed by using the same pipeline to identify unique CpGs. Each data point was generated with 4 subsamplings per dataset. The error bars represent s.d. The centre represents mean. n = 3 for LCM-RRBS, n = 8 for mRRBS, n = 2 for the rest.

    Journal: Nature biomedical engineering

    Article Title: Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

    doi:

    Figure Lengend Snippet: MID-RRBS generated high quality data using sub-1 ng DNA (a) The percentage of the theoretical maximum of CpGs covered at 1× and 10× coverage with starting DNA samples of various amounts. MspI in silico digestion followed by size selection of the hg19 genome produces the theoretical maximum of 2,782,793 CpGs. The centre represents mean. (b) Pearson’s correlations in the CG methylation level among various samples processed by MID-RRBS and Zymo kit. CpGs with ≥25× coverage were examined in the calculations. n = 14871. (c) MID-RRBS coverage of gene promoters (2 kb regions upstream of transcription starting sites of RefSeq genes), CpG islands (UCSC annotation database), CpG island shores (2 kb regions adjacent to CpG islands), enhancers (regions defined by H3K4me1+ H3K27ac based on ENCODE ChIP-seq data of GM12878 cells, ENCFF001SUE and ENCFF660QDF), and 5 kb tiles (non-overlapping consecutive 5 kb windows), in comparison to those of 1 μg and 1 ng samples processed by the Zymo kit. (d) The number of CpGs with various coverages (0–100×), in comparison to those of data produced using Zymo kit, mRRBS 30 , and LCM-RRBS 34 . (e) Saturation analysis of MID-RRBS data in comparison with other works. The analysis was conducted by random selection of a number of raw reads followed by using the same pipeline to identify unique CpGs. Each data point was generated with 4 subsamplings per dataset. The error bars represent s.d. The centre represents mean. n = 3 for LCM-RRBS, n = 8 for mRRBS, n = 2 for the rest.

    Article Snippet: PCR amplification and sequencing of single-cell RRBS samples The converted DNA (20 μl) was amplified by two rounds of PCR.

    Techniques: Generated, In Silico, Selection, Methylation, Chromatin Immunoprecipitation, Produced, Laser Capture Microdissection

    CG methylation levels across various annotated genomic features for NeuN+ and NeuN− fractions from mouse cerebellum (a) Box plots of CG methylation levels in promoters (n = 23525), intergenic regions (n = 19239), CpG islands (n = 16027), and CpG island shores (n = 30232). The boxes represent first quartile, median, and third quartile. Dots represent outliers. P-values are calculated using paired two-sided t-test and shown on top of the plots. (b) Scatter plots of CG methylation levels in promoters, intergenic regions, CpG islands, and CpG island shores. The MID-RRBS data were generated using 0.5 ng NeuN+/NeuN− DNA. r represents Pearson coefficient. R1 and R2 are two replicates.

    Journal: Nature biomedical engineering

    Article Title: Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

    doi:

    Figure Lengend Snippet: CG methylation levels across various annotated genomic features for NeuN+ and NeuN− fractions from mouse cerebellum (a) Box plots of CG methylation levels in promoters (n = 23525), intergenic regions (n = 19239), CpG islands (n = 16027), and CpG island shores (n = 30232). The boxes represent first quartile, median, and third quartile. Dots represent outliers. P-values are calculated using paired two-sided t-test and shown on top of the plots. (b) Scatter plots of CG methylation levels in promoters, intergenic regions, CpG islands, and CpG island shores. The MID-RRBS data were generated using 0.5 ng NeuN+/NeuN− DNA. r represents Pearson coefficient. R1 and R2 are two replicates.

    Article Snippet: PCR amplification and sequencing of single-cell RRBS samples The converted DNA (20 μl) was amplified by two rounds of PCR.

    Techniques: Methylation, Generated

    DNA methylation and expressional alterations of miR-340 ( a ) Relative expression of miR-340 in SK-N-BE and SHSY-5Y at 7 days post-ATRA. ( b,c ) Kaplan Meier survival plots for OS ( b ) and EFS ( c ) in 237 neuroblastoma tumors based on miR-340 expression. ( d ) SignalMap image from MeDIP analysis for the miR-340 upstream region. Only the methylation peak highlighted with a bracket (~6 Kb upstream) exhibited significant de-methylation in SK-N-BE cells 7 days post-ATRA. This peak overlaps the predicted TSS for miR-340. ( e ) Scatter plot of methylation vs. miR-340 expression in tumors showing a significant inverse correlation using Pearson’s correlation coefficient. ( f ) Expression of miR-340 following 5’-Aza-2 treatment of SK-N-BE and SHSY-5Y (*P

    Journal: Oncogene

    Article Title: Modulation of Neuroblastoma Disease Pathogenesis By An Extensive Network of Epigenetically Regulated MicroRNAs

    doi: 10.1038/onc.2012.311

    Figure Lengend Snippet: DNA methylation and expressional alterations of miR-340 ( a ) Relative expression of miR-340 in SK-N-BE and SHSY-5Y at 7 days post-ATRA. ( b,c ) Kaplan Meier survival plots for OS ( b ) and EFS ( c ) in 237 neuroblastoma tumors based on miR-340 expression. ( d ) SignalMap image from MeDIP analysis for the miR-340 upstream region. Only the methylation peak highlighted with a bracket (~6 Kb upstream) exhibited significant de-methylation in SK-N-BE cells 7 days post-ATRA. This peak overlaps the predicted TSS for miR-340. ( e ) Scatter plot of methylation vs. miR-340 expression in tumors showing a significant inverse correlation using Pearson’s correlation coefficient. ( f ) Expression of miR-340 following 5’-Aza-2 treatment of SK-N-BE and SHSY-5Y (*P

    Article Snippet: DNA methylation validation using Sequenom EpiTYPER mass spectroscopy Selected regions displaying differential methylation in MeDIP data were validated using Sequenom EpiTYPER mass spectroscopy analysis of bisulfite converted DNA ( ) (Sequenom, Hamburg, Germany).

    Techniques: DNA Methylation Assay, Expressing, Methylated DNA Immunoprecipitation, Methylation

    Overview of DNA methylation during thymocyte maturation. ( A ) Principal component analysis of all samples based on methylation profiles obtained from HM450 arrays. Arrows represent the direction of differentiation. ( B ) Venn diagrams showing all annotated DMRs at each differentiation step. ( C ) Genomic distribution of the thymic DMRs at each differentiation step using CIRCOS. Colored bars represent the Δ M -value. The gray lines intersect at Δ M = 0.

    Journal: Nucleic Acids Research

    Article Title: Regulation of the transcriptional program by DNA methylation during human αβ T-cell development

    doi: 10.1093/nar/gku1340

    Figure Lengend Snippet: Overview of DNA methylation during thymocyte maturation. ( A ) Principal component analysis of all samples based on methylation profiles obtained from HM450 arrays. Arrows represent the direction of differentiation. ( B ) Venn diagrams showing all annotated DMRs at each differentiation step. ( C ) Genomic distribution of the thymic DMRs at each differentiation step using CIRCOS. Colored bars represent the Δ M -value. The gray lines intersect at Δ M = 0.

    Article Snippet: Subsequently, whole genome methylation profiles were characterized by amplification of converted DNA and hybridization on Infinium HumanMethylation450 (HM450) BeadChips (Illumina Inc.) following Illumina's Infinium HD assay methylation protocol.

    Techniques: DNA Methylation Assay, Methylation

    Analysis of DNA methylation status of miR-200f promoter sequences in breast tumors. ( A ) Schematic depiction of miR- 200b-a-429 and miR-200c-141 genomic loci showing CpG islands (green), putative transcription start sites (TSS) and miRNA stem-loop sequences (red). The regions analyzed for DNA methylation (MassArray) are indicated by a black bar. Chromosomal location is indicated between brackets. ( B ) The DNA methylation levels across the regions shown in panel ( A ) were quantified in breast cancers by Sequenom MassArray® MALDI-TOF platform. The mean percentage of methylation levels in three tumor types (ER+, TN, MBC) are represented as box-plots. Statistical significance was determined by Student’s t test. ( C ) Expression and %CpG methylation data are represented on a scatter plot matrix showing correlation between the indicated variables, a 95% bivariate normal density ellipse is imposed on each scatterplot. Pearson correlation coefficients (R) and significance probabilities (P) are shown. Statistically significant p values (

    Journal: PLoS ONE

    Article Title: MicroRNA-200 Family Modulation in Distinct Breast Cancer Phenotypes

    doi: 10.1371/journal.pone.0047709

    Figure Lengend Snippet: Analysis of DNA methylation status of miR-200f promoter sequences in breast tumors. ( A ) Schematic depiction of miR- 200b-a-429 and miR-200c-141 genomic loci showing CpG islands (green), putative transcription start sites (TSS) and miRNA stem-loop sequences (red). The regions analyzed for DNA methylation (MassArray) are indicated by a black bar. Chromosomal location is indicated between brackets. ( B ) The DNA methylation levels across the regions shown in panel ( A ) were quantified in breast cancers by Sequenom MassArray® MALDI-TOF platform. The mean percentage of methylation levels in three tumor types (ER+, TN, MBC) are represented as box-plots. Statistical significance was determined by Student’s t test. ( C ) Expression and %CpG methylation data are represented on a scatter plot matrix showing correlation between the indicated variables, a 95% bivariate normal density ellipse is imposed on each scatterplot. Pearson correlation coefficients (R) and significance probabilities (P) are shown. Statistically significant p values (

    Article Snippet: Primers for PCR amplification of the converted DNA were designed using EpiDesigner® software (Sequenom, San Diego, CA, USA).

    Techniques: DNA Methylation Assay, Methylation, Expressing, CpG Methylation Assay

    Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of DNA (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 RT-PCR data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.

    Journal: PLoS ONE

    Article Title: Retrotransposon Hypomethylation in Melanoma and Expression of a Placenta-Specific Gene

    doi: 10.1371/journal.pone.0095840

    Figure Lengend Snippet: Mean promoter methylation for p KCNH5 . A . Genomic map of the p KCNH5 amplicon that was examined by Sequenom. Coordinates refer to the genomic location with respect to the p KCNH5 transcription start site. Red circles represent individual CpG sites. Black arrows represent primers used to amplify the 313 bp product, which contained 17 CpG sites that were analysed for methylation (all of which are located within the SINE ( AluY ) element). B . Columns represent mean CpG methylation for the amplicon. Solid bars represent Sequenom data from the present study and lined bars represent previously published Sequenom data [18] . In the present study, somatic and fetal tissues were quantified as pools of DNA (somatic pool: adult brain, kidney, heart, liver, spleen, pancreas, lung, colon and peripheral blood; fetal pool: fetal brain, liver, heart, stomach, and adrenal). In the previous study, somatic tissues (brain, kidney, heart, liver, spleen) and fetal tissues (brain, liver, heart, kidney and adrenal) were quantified as individual tissues; the lined bars represent mean methylation of these samples. Based on end-point p KCNH5 RT-PCR data (confirmed by sequencing), 11 melanoma samples express p KCNH5 (NZM09, NZM40, NZM06, NZM12, NZM15, NZM23, NZM53, NZM58, NZM52, NZM53T and NZM58T) and 17 samples did not express p KCNH5 . Error bars represent the 95% confidence interval of the mean.

    Article Snippet: PCR was performed directly on bisulphite converted DNA according to the manufacturer's protocol (Sequenom – San Diego, CA).

    Techniques: Methylation, Amplification, CpG Methylation Assay, Reverse Transcription Polymerase Chain Reaction, Sequencing