massarray epityper analysis Search Results


epityper massarray methylation analysis epityper massarray  (agena bioscience)
96
agena bioscience epityper massarray methylation analysis epityper massarray
Epityper Massarray Methylation Analysis Epityper Massarray, supplied by agena bioscience, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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massarray epityper  (Epigenomics ag)
90
Epigenomics ag massarray epityper
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Massarray Epityper, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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massarray-system-1  (agena bioscience)
96
agena bioscience massarray-system-1
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Massarray System 1, supplied by agena bioscience, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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methylation  (agena bioscience)
96
agena bioscience methylation
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Methylation, supplied by agena bioscience, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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massarray epityper platform  (Sequenom)
86
Sequenom massarray epityper platform
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Massarray Epityper Platform, supplied by Sequenom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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quantitative methylation analysis  (Sequenom)
86
Sequenom quantitative methylation analysis
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Quantitative Methylation Analysis, supplied by Sequenom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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epityper assay  (Sequenom)
86
Sequenom epityper assay
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Epityper Assay, supplied by Sequenom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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epityper software v1 0  (Sequenom)
86
Sequenom epityper software v1 0
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Epityper Software V1 0, supplied by Sequenom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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massarray compact maldi tof  (Sequenom)
86
Sequenom massarray compact maldi tof
a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using <t>MassArray</t> and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.
Massarray Compact Maldi Tof, supplied by Sequenom, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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humanmethylation450 beadchip 450k array  (INFINIUM Inc)
90
INFINIUM Inc humanmethylation450 beadchip 450k array
Comparison of methylation levels of peripheral blood DNA between different analytical methods.
Humanmethylation450 Beadchip 450k Array, supplied by INFINIUM Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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massarrayanalyzer 4 maldi tof mass spectrometer  (agena bioscience)
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agena bioscience massarrayanalyzer 4 maldi tof mass spectrometer
Comparison of methylation levels of peripheral blood DNA between different analytical methods.
Massarrayanalyzer 4 Maldi Tof Mass Spectrometer, supplied by agena bioscience, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using MassArray and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.

Journal: Nature genetics

Article Title: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

doi: 10.1038/s41588-017-0002-y

Figure Lengend Snippet: a , Schematic for analysis of 5mC, 5hmC and TET1 binding at the PAX6 locus. Arrows represent the P0 and P1 promoter, the grey box represents the PAX6 mRNA transcript and the black box represents the PAX6 protein. The region analyzed for 5mC using MassArray and for 5hmC using hMe-Seal profiling is shown by a green box. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. (NE D4) Neuroectoderm differentiation day 4; (NE D10) Neuroectoderm Differentiation day 10. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Diagram of homology-directed repair (HDR) of the TET1 locus in TKO hESCs. Red letters indicate mutations of the WT sequence. The sequences of the two repaired lines (TKO-r1, TKO-r2) are shown below. d , Mass spectrometry analysis of 5hmC levels in WT, TET KO mutant lines, lines in which one allele of TET1 has been repaired (TKO-R) and lines which underwent HDR targeting but retained the TKO mutations in the TET1 locus (TKO-nr). For all mass spectrometry analysis, 2 mutant lines were used for all genotypes except for TKO. For TKO lines, 2 different passages of the same line were used for mass spectrometry measurements. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, *** P <0.001. e , Analysis of percent 5hmC at the PAX6 P0 promoter by Epimark, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. f , Top panel: Analysis of 5hmC peak at the PAX6 P0 promoter by hMe-Seal in WT hESCs. Bottom panel: Analysis of TET1 peak at the PAX6 P0 promoter by TET1 ChIP-Seq in WT hESCs. Shaded area represents the region of the PAX6 P0 promoter assayed for 5hmC by Epimark ( e ) and TET1 binding by ChIP-qPCR ( g ). g , ChIP-qPCR for TET1 in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01, *** P <0.001. h , Analysis of 5hmC and TET1 peaks at bivalent promoters in WT hESCs. The height above the x-axis reflects the normalized tag count. i , Percent DNA methylation change (TKO – WT) in bivalent promoters that have 5hmC peaks compared to bivalent promoters that don’t have 5hmC peaks.

Article Snippet: MassArray Epityper analysis was performed using the WCMC Epigenomics core.

Techniques: Binding Assay, Sequencing, Mass Spectrometry, Mutagenesis, ChIP-sequencing, ChIP-qPCR, DNA Methylation Assay

a , Schema for rescue of the NE differentiation defect in TKO hESCs using PAX6 overexpression or targeted demethylation of the PAX6 P0 promoter. b , qPCR analysis of neuroectoderm ( SOX1 ) and pluripotency ( OCT4 ) markers in WT and TKO cells without doxycycline (TKO) and with doxycycline treatment (TKO +PAX6) at D10 of NE differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: one-way ANOVA, * P <0.05, ** P <0.01, *** P <0.001. c , Immunofluorescence of PAX6, SOX1 and OCT4 at the endpoint of differentiation (D10) of TKO cells without doxycycline treatment (TKO) and with doxycycline treatment (TKO + PAX6). Scale bar indicates 100 µm. d , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut (left) or a dCas9-TET1CD (right) fusion protein. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. Methylation analysis at the PAX6 P0 promoter was analyzed for these cell lines with and without doxycycline treatment, n = 3 independent experiments. Statistical analysis: Student’s t test (two sided), **** P <0.0001. e , qPCR of PAX6 expression on D10 of NE differentiation for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut or a dCas9-TET1CD fusion protein. PAX6 expression was analyzed for these cell lines with and without doxycycline treatment prior to differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), *** P <0.001. f , Immunofluorescence of PAX6 on D10 of NE differentiation for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut or a dCas9-TET1CD fusion protein. TKO hESCs expressing the dCas9-TET1CD fusion and a non-targeting gRNA were also used as a control. PAX6 immunofluorscence was analyzed for these cell lines with and without doxycycline treatment prior to differentiation. Scale bar indicates 100 µm.

Journal: Nature genetics

Article Title: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

doi: 10.1038/s41588-017-0002-y

Figure Lengend Snippet: a , Schema for rescue of the NE differentiation defect in TKO hESCs using PAX6 overexpression or targeted demethylation of the PAX6 P0 promoter. b , qPCR analysis of neuroectoderm ( SOX1 ) and pluripotency ( OCT4 ) markers in WT and TKO cells without doxycycline (TKO) and with doxycycline treatment (TKO +PAX6) at D10 of NE differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: one-way ANOVA, * P <0.05, ** P <0.01, *** P <0.001. c , Immunofluorescence of PAX6, SOX1 and OCT4 at the endpoint of differentiation (D10) of TKO cells without doxycycline treatment (TKO) and with doxycycline treatment (TKO + PAX6). Scale bar indicates 100 µm. d , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut (left) or a dCas9-TET1CD (right) fusion protein. The location of each row of CpGs with respect to the P0 TSS is shown to the left of the heat map. Methylation analysis at the PAX6 P0 promoter was analyzed for these cell lines with and without doxycycline treatment, n = 3 independent experiments. Statistical analysis: Student’s t test (two sided), **** P <0.0001. e , qPCR of PAX6 expression on D10 of NE differentiation for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut or a dCas9-TET1CD fusion protein. PAX6 expression was analyzed for these cell lines with and without doxycycline treatment prior to differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), *** P <0.001. f , Immunofluorescence of PAX6 on D10 of NE differentiation for TKO hESCs that express PAX6 targeting gRNAs with either a dCas9-TET1CD/Mut or a dCas9-TET1CD fusion protein. TKO hESCs expressing the dCas9-TET1CD fusion and a non-targeting gRNA were also used as a control. PAX6 immunofluorscence was analyzed for these cell lines with and without doxycycline treatment prior to differentiation. Scale bar indicates 100 µm.

Article Snippet: MassArray Epityper analysis was performed using the WCMC Epigenomics core.

Techniques: Over Expression, Immunofluorescence, Methylation, Expressing, Control

a , ChIP-qPCR for DNMT3B at the PAX6 locus in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter in WT, TKO and QKO hESCs. WT and TKO hESCs are passage-matched with the QKO hESCs. The location of each row of CpGs with respect to the TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. Quantification of the percent methylation is shown on the right, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Immunofluorescence of PAX6, SOX1 and OCT4 at D10 of NE differentiation in WT, TKO and QKO cells. Scale bar indicates 100 µm. d , qPCR analysis of neuroectoderm ( PAX6 and SOX1 ) and pluripotency ( OCT4 and NANOG ) markers in WT, TKO and QKO cells at D10 of NE differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, * P <0.05,** P <0.01,*** P <0.001, **** P <0.0001.

Journal: Nature genetics

Article Title: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

doi: 10.1038/s41588-017-0002-y

Figure Lengend Snippet: a , ChIP-qPCR for DNMT3B at the PAX6 locus in WT and TKO hESCs, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), * P <0.05, ** P <0.01. b , Heat map of MassArray analysis of 5mC at the PAX6 P0 promoter in WT, TKO and QKO hESCs. WT and TKO hESCs are passage-matched with the QKO hESCs. The location of each row of CpGs with respect to the TSS is shown to the left of the heat map. For each cell line three independent experiments are shown as three columns. Quantification of the percent methylation is shown on the right, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: Student’s t test (two sided), **** P <0.0001. c , Immunofluorescence of PAX6, SOX1 and OCT4 at D10 of NE differentiation in WT, TKO and QKO cells. Scale bar indicates 100 µm. d , qPCR analysis of neuroectoderm ( PAX6 and SOX1 ) and pluripotency ( OCT4 and NANOG ) markers in WT, TKO and QKO cells at D10 of NE differentiation, n = 3 independent experiments. Data presented are mean ± STD. Statistical analysis: black lines indicate comparisons to WT, one-way ANOVA, * P <0.05,** P <0.01,*** P <0.001, **** P <0.0001.

Article Snippet: MassArray Epityper analysis was performed using the WCMC Epigenomics core.

Techniques: ChIP-qPCR, Methylation, Immunofluorescence

Comparison of methylation levels of peripheral blood DNA between different analytical methods.

Journal: International Journal of Molecular Sciences

Article Title: Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals

doi: 10.3390/ijms19030900

Figure Lengend Snippet: Comparison of methylation levels of peripheral blood DNA between different analytical methods.

Article Snippet: Furthermore, we performed the Infinium HumanMethylation450 BeadChip (450K) array analysis using 48 sporadic BC cases and 48 healthy controls (cases and controls are the same from those of the MassARRAY EpiTYPER assay) and made a comparison with the published data.

Techniques: Comparison, Methylation, MassARRAY EpiTYPER assay