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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 403 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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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    92
    ATUM 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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    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
    EpigenDx bisulfite converted dna
    CGG-repeat instability in FX ESCs. a CGG-repeat size and methylation analysis for the WCMC37 ESCs and the individual lineages derived from it was done by MS_RPT-PCR followed by agarose gel electrophoresis as described in the “ Methods ” section. The “+” and “−“ signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp <t>DNA</t> size ladder and rpts, CGG repeats. b Pyrosequencing analysis of DNA methylation in the <t>FMR1</t> promoter of WCMC37 and 37A cells at passage 44 and 48, respectively. c qMS-PCR analysis of DNA methylation in the FMR1 promoter of the samples analyzed in a . The extent of methylation was determined by the ∆∆Ct method and the individual technical replicates varied by
    Bisulfite Converted Dna, supplied by EpigenDx, used in various techniques. Bioz Stars score: 92/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc bisulfite converted dna
    Stability of <t>DNA</t> methylation differences with cell passage. Three different IPF cell lines (A, B, and C) were assessed at passages 5, 6, and 7, and the DNA methylation for each cell line and each passage was compared. A) Shown are the methylation level of <t>CpG</t> sites 8, 9, and 10 in the upstream segment of the CARD10 promoter for IPF cell lines A and B at serial passage. B) Shown are the methylation levels of CpG sites 7–14 of the MGMT promoter for IPF cell lines A–C at serial passage.
    Bisulfite Converted Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 2091 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Promega bisulfite converted dna
    Stability of <t>DNA</t> methylation differences with cell passage. Three different IPF cell lines (A, B, and C) were assessed at passages 5, 6, and 7, and the DNA methylation for each cell line and each passage was compared. A) Shown are the methylation level of <t>CpG</t> sites 8, 9, and 10 in the upstream segment of the CARD10 promoter for IPF cell lines A and B at serial passage. B) Shown are the methylation levels of CpG sites 7–14 of the MGMT promoter for IPF cell lines A–C at serial passage.
    Bisulfite Converted Dna, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 186 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Pacific Biosciences bisulfite converted dna
    Epigenetics measurement techniques. A wide variety of methods characterize epigenetic alterations. Currently, the most common genome-wide approaches identify nucleosome-free regions (DNaseI-Seq; MNase-Seq; FAIRE-Seq; ATAC-Seq), protein-mediated <t>DNA</t> interaction sites (Hi-C; 5-C), histone marks and DNA-binding proteins (ChIP-Seq; ChIA-PET) and DNA methylation (array hybridization, WGBS, MBD-Seq, <t>PacBio,</t> nanopore). (A colour version of this figure is available online at: https://academic.oup.com/bfg )
    Bisulfite Converted Dna, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher bisulfite converted dna
    Epigenetics measurement techniques. A wide variety of methods characterize epigenetic alterations. Currently, the most common genome-wide approaches identify nucleosome-free regions (DNaseI-Seq; MNase-Seq; FAIRE-Seq; ATAC-Seq), protein-mediated <t>DNA</t> interaction sites (Hi-C; 5-C), histone marks and DNA-binding proteins (ChIP-Seq; ChIA-PET) and DNA methylation (array hybridization, WGBS, MBD-Seq, <t>PacBio,</t> nanopore). (A colour version of this figure is available online at: https://academic.oup.com/bfg )
    Bisulfite Converted Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1153 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Genewiz bisulfite converted dna
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
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    92
    Diagenode control genomic unmethylated bisulfite converted dna
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
    Control Genomic Unmethylated Bisulfite Converted Dna, supplied by Diagenode, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc sodium bisulfite converted bs dna
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
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    85
    Millipore bisulfite converted cpgenome universal methylated dna
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
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    93
    Roche bisulfite converted dna pool
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
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    99
    Qiagen bisulfite converted human control dna
    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative <t>RT-PCR.</t> P -values were calculated by t-test . <t>DNA</t> methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1
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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

    Comparison of DNA copy numbers obtained using different techniques. DNA copy numbers of methylated/unmethylated DNA standards based on specifications of manufacturer (Expected), measured by flourometer and of p14 by Restriction Enzyme (RE) dPCR and p14 and COL2A1 with MethyLight dPCR in the 0% and 100% methylated samples. Copy numbers shown were obtained from 5 ng starting material (based on expected DNA quantity), pre-bisulfite conversion and RE digestion. RE dPCR data shows p14 copy number from the mock, MSRE and MDRE treatments. MethyLight dPCR data shows copy number obtained using the p14_M assay in singleplex and the methylation independent control COL2A1. Statistical comparisons are for Student’s t-test (* = p

    Journal: BMC Genomics

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis

    doi: 10.1186/1471-2164-15-1174

    Figure Lengend Snippet: Comparison of DNA copy numbers obtained using different techniques. DNA copy numbers of methylated/unmethylated DNA standards based on specifications of manufacturer (Expected), measured by flourometer and of p14 by Restriction Enzyme (RE) dPCR and p14 and COL2A1 with MethyLight dPCR in the 0% and 100% methylated samples. Copy numbers shown were obtained from 5 ng starting material (based on expected DNA quantity), pre-bisulfite conversion and RE digestion. RE dPCR data shows p14 copy number from the mock, MSRE and MDRE treatments. MethyLight dPCR data shows copy number obtained using the p14_M assay in singleplex and the methylation independent control COL2A1. Statistical comparisons are for Student’s t-test (* = p

    Article Snippet: For MethyLight qPCR, quantification was performed using the standard curve method with Bisulfite Converted Methylated Human DNA from Zymo Research.

    Techniques: Methylation, Digital PCR

    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

    CGG-repeat instability in FX ESCs. a CGG-repeat size and methylation analysis for the WCMC37 ESCs and the individual lineages derived from it was done by MS_RPT-PCR followed by agarose gel electrophoresis as described in the “ Methods ” section. The “+” and “−“ signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. b Pyrosequencing analysis of DNA methylation in the FMR1 promoter of WCMC37 and 37A cells at passage 44 and 48, respectively. c qMS-PCR analysis of DNA methylation in the FMR1 promoter of the samples analyzed in a . The extent of methylation was determined by the ∆∆Ct method and the individual technical replicates varied by

    Journal: Molecular Autism

    Article Title: CGG-repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells and stem cell-derived neurons

    doi: 10.1186/s13229-016-0105-9

    Figure Lengend Snippet: CGG-repeat instability in FX ESCs. a CGG-repeat size and methylation analysis for the WCMC37 ESCs and the individual lineages derived from it was done by MS_RPT-PCR followed by agarose gel electrophoresis as described in the “ Methods ” section. The “+” and “−“ signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. b Pyrosequencing analysis of DNA methylation in the FMR1 promoter of WCMC37 and 37A cells at passage 44 and 48, respectively. c qMS-PCR analysis of DNA methylation in the FMR1 promoter of the samples analyzed in a . The extent of methylation was determined by the ∆∆Ct method and the individual technical replicates varied by

    Article Snippet: Additionally, DNA methylation at 22 CpG residues in the FMR1 promoter in WCMC37 p45 cells was also analyzed by pyrosequencing of bisulfite-converted DNA by EpigenDx, Inc. (Hopkinton, MA) using assays ADS1451-FS1 and ADS1451-FS2.

    Techniques: Methylation, Derivative Assay, Mass Spectrometry, Polymerase Chain Reaction, Agarose Gel Electrophoresis, DNA Methylation Assay

    Unmethylated FM alleles do not become silenced on differentiation into neurons. The repeat size, methylation status, and FMR1 mRNA levels of the indicated cultures were monitored as described in the “ Methods ” section. The “+” and “−” signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. A late passage culture of 37D ESCs containing little, if any methylated alleles, was differentiated into neurons as described in the “ Methods ” section. Methylation levels were measured by qMS-PCR on the indicated number of days after the initiation of neuronal differentiation. See Additional file 3 : Figure S3 for representative images during neuronal differentiation of 37D cells

    Journal: Molecular Autism

    Article Title: CGG-repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells and stem cell-derived neurons

    doi: 10.1186/s13229-016-0105-9

    Figure Lengend Snippet: Unmethylated FM alleles do not become silenced on differentiation into neurons. The repeat size, methylation status, and FMR1 mRNA levels of the indicated cultures were monitored as described in the “ Methods ” section. The “+” and “−” signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. A late passage culture of 37D ESCs containing little, if any methylated alleles, was differentiated into neurons as described in the “ Methods ” section. Methylation levels were measured by qMS-PCR on the indicated number of days after the initiation of neuronal differentiation. See Additional file 3 : Figure S3 for representative images during neuronal differentiation of 37D cells

    Article Snippet: Additionally, DNA methylation at 22 CpG residues in the FMR1 promoter in WCMC37 p45 cells was also analyzed by pyrosequencing of bisulfite-converted DNA by EpigenDx, Inc. (Hopkinton, MA) using assays ADS1451-FS1 and ADS1451-FS2.

    Techniques: Methylation, Polymerase Chain Reaction

    Selective growth advantage of cells carrying methylated FMR1 alleles with large CGG repeats. a – c The repeat size, methylation status, and FMR1 mRNA levels of the indicated cultures were monitored as described in the “ Methods ” section. The “+” and “−” signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. a , b Data for 37D and 37A lineages that were maintained in culture for extended periods of time. The DNA methylation status is indicated by the grey line and symbols in the right hand panel, and the mRNA level is indicated by the black line and symbols . c Growth of methylated 37A and unmethylated 37D cells. Late passage 37A cells that were completely methylated and late passage 37D cells that were unmethylated were either grown separately ( i ) or in a ~1:1 mixture ( ii ) for ~20 passages. S refers to the cells at the start of the experiment and E to the cells at the end of the experiment. Data for the mixed cultures are shown from two independent experiments (Rep 1 and Rep 2). Panel ( iii ) shows the DNA methylation for each set of cultures at the start and end of the experiment as an average from two experiments and the error bars indicate standard deviation

    Journal: Molecular Autism

    Article Title: CGG-repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells and stem cell-derived neurons

    doi: 10.1186/s13229-016-0105-9

    Figure Lengend Snippet: Selective growth advantage of cells carrying methylated FMR1 alleles with large CGG repeats. a – c The repeat size, methylation status, and FMR1 mRNA levels of the indicated cultures were monitored as described in the “ Methods ” section. The “+” and “−” signs indicate the presence or absence of predigestion by the methylation-sensitive restriction enzyme, HpaII. M, 100-bp DNA size ladder and rpts, CGG repeats. a , b Data for 37D and 37A lineages that were maintained in culture for extended periods of time. The DNA methylation status is indicated by the grey line and symbols in the right hand panel, and the mRNA level is indicated by the black line and symbols . c Growth of methylated 37A and unmethylated 37D cells. Late passage 37A cells that were completely methylated and late passage 37D cells that were unmethylated were either grown separately ( i ) or in a ~1:1 mixture ( ii ) for ~20 passages. S refers to the cells at the start of the experiment and E to the cells at the end of the experiment. Data for the mixed cultures are shown from two independent experiments (Rep 1 and Rep 2). Panel ( iii ) shows the DNA methylation for each set of cultures at the start and end of the experiment as an average from two experiments and the error bars indicate standard deviation

    Article Snippet: Additionally, DNA methylation at 22 CpG residues in the FMR1 promoter in WCMC37 p45 cells was also analyzed by pyrosequencing of bisulfite-converted DNA by EpigenDx, Inc. (Hopkinton, MA) using assays ADS1451-FS1 and ADS1451-FS2.

    Techniques: Methylation, DNA Methylation Assay, Standard Deviation

    Stability of DNA methylation differences with cell passage. Three different IPF cell lines (A, B, and C) were assessed at passages 5, 6, and 7, and the DNA methylation for each cell line and each passage was compared. A) Shown are the methylation level of CpG sites 8, 9, and 10 in the upstream segment of the CARD10 promoter for IPF cell lines A and B at serial passage. B) Shown are the methylation levels of CpG sites 7–14 of the MGMT promoter for IPF cell lines A–C at serial passage.

    Journal: PLoS ONE

    Article Title: Lung Fibroblasts from Patients with Idiopathic Pulmonary Fibrosis Exhibit Genome-Wide Differences in DNA Methylation Compared to Fibroblasts from Nonfibrotic Lung

    doi: 10.1371/journal.pone.0107055

    Figure Lengend Snippet: Stability of DNA methylation differences with cell passage. Three different IPF cell lines (A, B, and C) were assessed at passages 5, 6, and 7, and the DNA methylation for each cell line and each passage was compared. A) Shown are the methylation level of CpG sites 8, 9, and 10 in the upstream segment of the CARD10 promoter for IPF cell lines A and B at serial passage. B) Shown are the methylation levels of CpG sites 7–14 of the MGMT promoter for IPF cell lines A–C at serial passage.

    Article Snippet: Bisulfite-converted DNA was analyzed for methylation at 27,578 CpG sites using the Illumina (San Diego, California) HumanMethylation27 BeadChip Array according to the manufacturer’s protocol.

    Techniques: DNA Methylation Assay, Methylation

    Methylation levels of CDKN2B , CARD10 , and MGMT by bisulfite sequencing in IPF and nonfibrotic control fibroblasts. The DNA methylation levels of various CpG sites within the CDKN2B (A), CARD10 (B), and MGMT (C) genes were analyzed by bisulfite pyrosequencing in fibroblasts from IPF (n = 6) and nonfibrotic control patients (n = 3). The hashtag indicates the CpG site that was assayed and identified to be differentially methylated by the array. Illustrated are the location of the CpG sites analyzed (based on NCBI Build 36.1) and position relative to the gene location, theoretical CpG islands, and MeDIP-Seq data from UCSC Genome Browser. *P

    Journal: PLoS ONE

    Article Title: Lung Fibroblasts from Patients with Idiopathic Pulmonary Fibrosis Exhibit Genome-Wide Differences in DNA Methylation Compared to Fibroblasts from Nonfibrotic Lung

    doi: 10.1371/journal.pone.0107055

    Figure Lengend Snippet: Methylation levels of CDKN2B , CARD10 , and MGMT by bisulfite sequencing in IPF and nonfibrotic control fibroblasts. The DNA methylation levels of various CpG sites within the CDKN2B (A), CARD10 (B), and MGMT (C) genes were analyzed by bisulfite pyrosequencing in fibroblasts from IPF (n = 6) and nonfibrotic control patients (n = 3). The hashtag indicates the CpG site that was assayed and identified to be differentially methylated by the array. Illustrated are the location of the CpG sites analyzed (based on NCBI Build 36.1) and position relative to the gene location, theoretical CpG islands, and MeDIP-Seq data from UCSC Genome Browser. *P

    Article Snippet: Bisulfite-converted DNA was analyzed for methylation at 27,578 CpG sites using the Illumina (San Diego, California) HumanMethylation27 BeadChip Array according to the manufacturer’s protocol.

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

    Methylation differences between IPF fibroblasts and two groups of nonfibrotic control cells. Levels of DNA methylation were analyzed using the HumanMethylation27 array in 6 IPF fibroblast lines, 3 patient-derived nonfibrotic controls, and 3 commercially available nonfibrotic cell lines (CCL190, CCL204, and CCL210). A) The number of differentially methylated CpG loci between IPF and patient-derived controls, between IPF and commercial cell line controls, and the overlap of these differences are shown. B) Fraction of differentially methylated CpG loci that are within and outside of CpG islands.

    Journal: PLoS ONE

    Article Title: Lung Fibroblasts from Patients with Idiopathic Pulmonary Fibrosis Exhibit Genome-Wide Differences in DNA Methylation Compared to Fibroblasts from Nonfibrotic Lung

    doi: 10.1371/journal.pone.0107055

    Figure Lengend Snippet: Methylation differences between IPF fibroblasts and two groups of nonfibrotic control cells. Levels of DNA methylation were analyzed using the HumanMethylation27 array in 6 IPF fibroblast lines, 3 patient-derived nonfibrotic controls, and 3 commercially available nonfibrotic cell lines (CCL190, CCL204, and CCL210). A) The number of differentially methylated CpG loci between IPF and patient-derived controls, between IPF and commercial cell line controls, and the overlap of these differences are shown. B) Fraction of differentially methylated CpG loci that are within and outside of CpG islands.

    Article Snippet: Bisulfite-converted DNA was analyzed for methylation at 27,578 CpG sites using the Illumina (San Diego, California) HumanMethylation27 BeadChip Array according to the manufacturer’s protocol.

    Techniques: Methylation, DNA Methylation Assay, Derivative Assay

    Variability in DNA methylation of IPF cells. A) Heirarchical cluster analysis was performed in each cell line studied, which also includes 3 separate samples of IMR-90 cells, a primary fetal fibroblast cell line. The mean methylation levels of the upstream CARD10 promoter (B) and the methylation levels of the individual CpG sites in the MGMT promoter (C) were compared among each individual IPF cell line and nonfibrotic cell lines.

    Journal: PLoS ONE

    Article Title: Lung Fibroblasts from Patients with Idiopathic Pulmonary Fibrosis Exhibit Genome-Wide Differences in DNA Methylation Compared to Fibroblasts from Nonfibrotic Lung

    doi: 10.1371/journal.pone.0107055

    Figure Lengend Snippet: Variability in DNA methylation of IPF cells. A) Heirarchical cluster analysis was performed in each cell line studied, which also includes 3 separate samples of IMR-90 cells, a primary fetal fibroblast cell line. The mean methylation levels of the upstream CARD10 promoter (B) and the methylation levels of the individual CpG sites in the MGMT promoter (C) were compared among each individual IPF cell line and nonfibrotic cell lines.

    Article Snippet: Bisulfite-converted DNA was analyzed for methylation at 27,578 CpG sites using the Illumina (San Diego, California) HumanMethylation27 BeadChip Array according to the manufacturer’s protocol.

    Techniques: DNA Methylation Assay, Methylation

    Epigenetics measurement techniques. A wide variety of methods characterize epigenetic alterations. Currently, the most common genome-wide approaches identify nucleosome-free regions (DNaseI-Seq; MNase-Seq; FAIRE-Seq; ATAC-Seq), protein-mediated DNA interaction sites (Hi-C; 5-C), histone marks and DNA-binding proteins (ChIP-Seq; ChIA-PET) and DNA methylation (array hybridization, WGBS, MBD-Seq, PacBio, nanopore). (A colour version of this figure is available online at: https://academic.oup.com/bfg )

    Journal: Briefings in Functional Genomics

    Article Title: Epigenetic regulation of gene expression in cancer: techniques, resources and analysis

    doi: 10.1093/bfgp/elx018

    Figure Lengend Snippet: Epigenetics measurement techniques. A wide variety of methods characterize epigenetic alterations. Currently, the most common genome-wide approaches identify nucleosome-free regions (DNaseI-Seq; MNase-Seq; FAIRE-Seq; ATAC-Seq), protein-mediated DNA interaction sites (Hi-C; 5-C), histone marks and DNA-binding proteins (ChIP-Seq; ChIA-PET) and DNA methylation (array hybridization, WGBS, MBD-Seq, PacBio, nanopore). (A colour version of this figure is available online at: https://academic.oup.com/bfg )

    Article Snippet: Additional methods are also developing to address the challenges of aligning bisulfite-converted DNA, including PacBio or single-molecule real-time (SMRT) sequencing and nanopore sequencing.

    Techniques: Genome Wide, Hi-C, DNA Binding Assay, Chromatin Immunoprecipitation, ChIA Pet Assay, DNA Methylation Assay, Hybridization

    Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative RT-PCR. P -values were calculated by t-test . DNA methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1

    Journal: Oncotarget

    Article Title: Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC

    doi: 10.18632/oncotarget.14856

    Figure Lengend Snippet: Differential expression and methylation of DTX1 , BANK1 and BIN2 in the validation cohort Gene expression ( A ) was evaluated by quantitative RT-PCR. P -values were calculated by t-test . DNA methylation ( B ) was evaluated by bisulfite sequencing. Box color-code: white–unmethylated (hypomethylated); grey–hemimethylated, black–hypermethylated. P -values were calculated by Fisher exact test, as unmethylated signal vs methylated signal (hemi- or hypermethylated) in two groups. P -values for DTX1 = 0.105, for BANK1

    Article Snippet: The purified PCR product from bisulfite-converted DNA for each sample and gene was sequenced (Genewiz, South Plainfield, NJ).

    Techniques: Expressing, Methylation, Quantitative RT-PCR, DNA Methylation Assay, Methylation Sequencing