mass spectrometry-based dna methylation profiling sequenom massarray epityper (Sequenom)

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Sequenom mass spectrometry-based dna methylation profiling sequenom massarray epityper

<t>Monoallelic</t> <t>methylation</t> of the human DNMT1 gene. A , location of the DNMT1 CpG island/promoter <t>DNA</t> methylation assays used for bisulfite sequencing. Genomic coordinates on chromosome 19 are shown, along with location of individual CpG dinucleotides ( dashes ) and CpG island location ( gray bar ) in relation to the DNMT 1 gene (exon 1 shown as a blue box , intron shown as an arrowed line ) according to the University of California Santa Cruz genome browser (hg_18 assembly). The arrows denote transcriptional direction. The location of rs8112895 SNP in the DNMT1_assay_4 is also shown. B , representative DNA methylation of a single full term human placental sample for assay_1 ( i ) and assay_4 ( ii ) showing a monoallelic pattern of methylation within the human placenta. Between eight and 12 individual clones were sequenced for each sample. The circles correspond to CpG sites denoted by black dashes in A. Closed circles , methylation; open circles , lack of methylation. Mean methylation levels seen at each CpG site in multiple placental samples for each assay are shown as shaded bars between 0 and 100% ( n = 4). Missing circles indicate CpG sites for which no information was obtained. C , DNMT1_4 methylation assay spanning SNP rs8112895 was used for bisulfite sequencing methylation analysis in purified first trimester cytotrophoblast cells. i , reference genomic DNA sequence surrounding rs8112895 SNP ( R ) and CpG dinucleotides ( boxed ). ii , individual clone sequences showing the presence of bisulfite-converted CG sites ( TG ) and unconverted CG sites ( CG ) in both maternal and paternal alleles from this heterozygous sample. This confirms a lack of parent of origin of the observed DNMT1 promoter methylation.

Mass Spectrometry Based Dna Methylation Profiling Sequenom Massarray Epityper, supplied by Sequenom, 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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Average 90 stars, based on 1 article reviews

mass spectrometry-based dna methylation profiling sequenom massarray epityper - by Bioz Stars, 2026-09

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1) Product Images from "DNA Methylation-mediated Down-regulation of DNA Methyltransferase-1 ( DNMT1 ) Is Coincident with, but Not Essential for, Global Hypomethylation in Human Placenta "

Article Title: DNA Methylation-mediated Down-regulation of DNA Methyltransferase-1 ( DNMT1 ) Is Coincident with, but Not Essential for, Global Hypomethylation in Human Placenta

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M109.064956

Monoallelic methylation of the human DNMT1 gene. A , location of the DNMT1 CpG island/promoter DNA methylation assays used for bisulfite sequencing. Genomic coordinates on chromosome 19 are shown, along with location of individual CpG dinucleotides ( dashes ) and CpG island location ( gray bar ) in relation to the DNMT 1 gene (exon 1 shown as a blue box , intron shown as an arrowed line ) according to the University of California Santa Cruz genome browser (hg_18 assembly). The arrows denote transcriptional direction. The location of rs8112895 SNP in the DNMT1_assay_4 is also shown. B , representative DNA methylation of a single full term human placental sample for assay_1 ( i ) and assay_4 ( ii ) showing a monoallelic pattern of methylation within the human placenta. Between eight and 12 individual clones were sequenced for each sample. The circles correspond to CpG sites denoted by black dashes in A. Closed circles , methylation; open circles , lack of methylation. Mean methylation levels seen at each CpG site in multiple placental samples for each assay are shown as shaded bars between 0 and 100% ( n = 4). Missing circles indicate CpG sites for which no information was obtained. C , DNMT1_4 methylation assay spanning SNP rs8112895 was used for bisulfite sequencing methylation analysis in purified first trimester cytotrophoblast cells. i , reference genomic DNA sequence surrounding rs8112895 SNP ( R ) and CpG dinucleotides ( boxed ). ii , individual clone sequences showing the presence of bisulfite-converted CG sites ( TG ) and unconverted CG sites ( CG ) in both maternal and paternal alleles from this heterozygous sample. This confirms a lack of parent of origin of the observed DNMT1 promoter methylation.

Figure Legend Snippet: Monoallelic methylation of the human DNMT1 gene. A , location of the DNMT1 CpG island/promoter DNA methylation assays used for bisulfite sequencing. Genomic coordinates on chromosome 19 are shown, along with location of individual CpG dinucleotides ( dashes ) and CpG island location ( gray bar ) in relation to the DNMT 1 gene (exon 1 shown as a blue box , intron shown as an arrowed line ) according to the University of California Santa Cruz genome browser (hg_18 assembly). The arrows denote transcriptional direction. The location of rs8112895 SNP in the DNMT1_assay_4 is also shown. B , representative DNA methylation of a single full term human placental sample for assay_1 ( i ) and assay_4 ( ii ) showing a monoallelic pattern of methylation within the human placenta. Between eight and 12 individual clones were sequenced for each sample. The circles correspond to CpG sites denoted by black dashes in A. Closed circles , methylation; open circles , lack of methylation. Mean methylation levels seen at each CpG site in multiple placental samples for each assay are shown as shaded bars between 0 and 100% ( n = 4). Missing circles indicate CpG sites for which no information was obtained. C , DNMT1_4 methylation assay spanning SNP rs8112895 was used for bisulfite sequencing methylation analysis in purified first trimester cytotrophoblast cells. i , reference genomic DNA sequence surrounding rs8112895 SNP ( R ) and CpG dinucleotides ( boxed ). ii , individual clone sequences showing the presence of bisulfite-converted CG sites ( TG ) and unconverted CG sites ( CG ) in both maternal and paternal alleles from this heterozygous sample. This confirms a lack of parent of origin of the observed DNMT1 promoter methylation.

Techniques Used: Methylation, DNA Methylation Assay, Methylation Sequencing, Clone Assay, Purification, Sequencing

DNMT1 promoter methylation is restricted to primates. Bisulfite DNA sequencing confirmed promoter methylation of the DNMT1 gene in full term baboon ( A ) and marmoset ( B ) placental tissue, with no evidence for methylation in mouse ( C ), bovine, or guinea pig placental tissue (data not shown).

Figure Legend Snippet: DNMT1 promoter methylation is restricted to primates. Bisulfite DNA sequencing confirmed promoter methylation of the DNMT1 gene in full term baboon ( A ) and marmoset ( B ) placental tissue, with no evidence for methylation in mouse ( C ), bovine, or guinea pig placental tissue (data not shown).

Techniques Used: Methylation, DNA Sequencing

Methylation:

Article Title: Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis.
Article Snippet: Further, we have performed multiple repeats in our Sequenom EpiTyper methylation analysis to provide a measure of technical variation in this process. .. In general, we see significant concordance between RRBS and Sequenom EpiTyper methylation patterns. .. Our observations are consistent with previous studies that demonstrated Sequenom EpiTyper platform to be a reliable targeted approach to validate genome-wide methylation data generated from RRBS [13–15].

Article Title: Methylation of the SLC6a2 Gene Promoter in Major Depression and Panic Disorder
Article Snippet: .. Promoter methylation of the SLC6a2 gene was also investigated using EpiTYPER methylation analysis on the MassARRAY® platform (Sequenom). ..

Article Title: DMAP2: A Pipeline for Analysis of Whole-Genome-Scale DNA Methylation Sequencing Data.
Article Snippet: .. Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis. .. Epigenomics, 9(6), 823–832. https://doi.org/ 10.2217/epi-2016-0176 Chatterjee, A., Macaulay, E. C., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., Devenish, C. J., & Morison, I. M. (2016).

Article Title: Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes.
Article Snippet: .. Several genes have been selected for validation by Quantitative methylation MassArray EpiTyper (Sequenom, San Diego, CA, U.S.) and here we choose to present the result of one gene i.e. WT1. ..

Article Title: Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis.
Article Snippet: Our observations are consistent with previous studies that demonstrated Sequenom EpiTyper platform to be a reliable targeted approach to validate genome-wide methylation data generated from RRBS [13–15]. .. By comparing RRBS and Sequenom EpiTyper methylation data, we demonstrate that methylation values between the two techniques are in better agreement if regions containing multiple CpG sites are compared instead of regions containing single CpG sites. ..

other:

Article Title: Comprehensive interrogation of CpG island methylation in the gene encoding COMT, a key estrogen and catecholamine regulator
Article Snippet: The SEQUENOM EpiTYPER ® methylation assay has been validated in numerous studies and previously described in detail [ - ].

DNA Methylation Assay:

Article Title: Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis.
Article Snippet: .. Sequenom EpiTyper DNA methylation assay The primers used for analyzing four genes described here were designed using the EpiTyper assay designer [25]. ..

Methylation Sequencing:

Biomarker Discovery:

EpiTYPER Assay: