Journal: PLoS ONE

Article Title: Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women

doi: 10.1371/journal.pone.0124340

Figure Lengend Snippet: Box plots illustrating the DNA methylation of the miRNA genes investigated. The names of the miRNA MassARRAY amplicons analyzed by Sequenom are displayed at the top of each plot. The p-value (Wilcoxon test) for each amplicon analyzed is displayed on the second line at the top of the plot. The x-axis is divided into the two interval groups; early, representing Ella FFPE samples ≤ 5.2 years postpartum, and late, representing Ella FFPE samples ≥ 5.3 years postpartum. The y-axis represents the mean DNA methylation (%) of the amplicon.

Article Snippet: To detect DNA methylation across miRNA regulatory regions we used the Sequenom MassARRAY platform.

Techniques: DNA Methylation Assay, Amplification

Journal: PLoS ONE

Article Title: Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women

doi: 10.1371/journal.pone.0124340

Figure Lengend Snippet: The x-axis shows the mean DNA methylation (%) of the miRNA Sequenom MassARRAY amplicons. The y-axis shows the miRNA expression levels as determined by quantitative RT-PCR analysis. The names of miRNA genes analyzed by MassARRAY and the names of the respective mature miRNA products detected by quantitative RT-PCR are displayed at the top of each plot. The Spearman correlation coefficient rho and the p-value (two-sided) of the correlation are displayed on the second line at the top of each plot.

Article Snippet: To detect DNA methylation across miRNA regulatory regions we used the Sequenom MassARRAY platform.

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

Journal: Multiple sclerosis and related disorders

Article Title: Ultra-high field spinal cord MRI in multiple sclerosis: Where are we standing? A literature review.

doi: 10.1016/j.msard.2021.103436

Figure Lengend Snippet: Fig. 4. Cd interfered with the DNA methylation of Oct4 and Nanog of mouse ES cells into ovarian GCs. A and E represented the methylation status of CpG islands on DNA templates in the promoter regions of both factors was evaluated using the Sequenom MassARRAY Methylation. B and F: DNA methylation rate of CpG locus in the promoter region of different sites of both factors. C–K represented the degree of DNA methylation on different fragments of the factors in maps and DNA methylation rate in the promoter region in each fragment and groups. Data are presented as the mean ± SD, *P < 0.05 compared with the IA group.

Article Snippet: The DNA methylation levels of the upstream promoter regions of the four markers were detected by the Sequenom MassARRAY Methylation method combined with the dedicated analysis software MethPrimer.

Techniques: DNA Methylation Assay, Methylation

Journal: Multiple sclerosis and related disorders

Article Title: Ultra-high field spinal cord MRI in multiple sclerosis: Where are we standing? A literature review.

doi: 10.1016/j.msard.2021.103436

Figure Lengend Snippet: Fig. 5. Cd interfered with the DNA methylation of Amhr2 and Sox2 of mouse ES cells into ovarian GCs. A and E represented the methylation status of CpG islands on DNA templates in the promoter regions of both factors was evaluated using the Sequenom MassARRAY Methylation. B and F: DNA methylation rate of CpG locus in the promoter region of different sites of both factors. C-K represented the degree of DNA methylation on different fragments of the factors in maps and DNA methylation rate in the promoter region in each fragment and groups. Data are presented as the mean ± SD, *P < 0.05 compared with the IA group.

Article Snippet: The DNA methylation levels of the upstream promoter regions of the four markers were detected by the Sequenom MassARRAY Methylation method combined with the dedicated analysis software MethPrimer.

Techniques: DNA Methylation Assay, Methylation

Journal: Scientific Reports

Article Title: A novel strategy for forensic age prediction by DNA methylation and support vector regression model

doi: 10.1038/srep17788

Figure Lengend Snippet: ( a ) The reliability of the Sequenom MassARRAY output data. The confidence of methylation values for each product of primer per sample was assigned to a value referring to low (0) to high confidence (5). This value > 1.9 showed that the methylation level can be accepted. Our data from Sequenom MassARRAY is of high quality since 95% values were accepted. ( b ) Scatter plots of the methylation level as a function of age for 11 CpG sites that were selected from the Sequenom MassARRAY result at |R| < 0.5. The ID of CpG sites and their R values are shown in the right top corner of each sub-figure.

Article Snippet: Detection of DNA methylation levels of specific sites was performed by Sequenom MassARRAY platform (Sequenom).

Techniques: Methylation

Journal: Scientific Reports

Article Title: A novel strategy for forensic age prediction by DNA methylation and support vector regression model

doi: 10.1038/srep17788

Figure Lengend Snippet: ( a ) Multivariate linear regression model. ( b ) Multivariate nonlinear regression model. ( c ) Back propagation neural network model. (d) Support vector regression model. Using 11 CpG sites selected from Sequenom MassARRAY results in 49 females, the mean absolute deviation for each method was 6.4, 4.1, 3.9, and 2 years, respectively.

Article Snippet: Detection of DNA methylation levels of specific sites was performed by Sequenom MassARRAY platform (Sequenom).

Techniques: Plasmid Preparation

Journal: Scientific Reports

Article Title: A novel strategy for forensic age prediction by DNA methylation and support vector regression model

doi: 10.1038/srep17788

Figure Lengend Snippet: ( a ) The minimal MAD of predicted age as a function of the number of sites that compose the independent variables. The 11 CpG sites selected from the Sequenom MassARRAY dataset were combined to one to 11 independent variables. SVR model fit on all but one sample, and the minimal MAD of the predicted age was observed for a given number of independent variables. ( b ) Predicted versus observed age of all 49 subjects, using SVR model by six markers. MAD of 2.8 years was observed, which is slightly higher than that obtained by 11 markers. ( c ) Predicted versus observed age using multivariate linear regression by three DNA methylation markers obtained from a recent study . The original BeadChip data of these three sites were extracted to predict age by using a multivariate linear regression model, and an MAD of 6.27 years was obtained. ( d ) Predicted versus observed age using SVR by three DNA methylation markers obtained from a recent study . MAD of 4.23 years was obtained, which is better than the MAD obtained when using a multivariate linear regression (panel C), and better than the MAD obtained when using a multivariate linear regression based on pyrosequencing data in the published study (5.4 years) .

Article Snippet: Detection of DNA methylation levels of specific sites was performed by Sequenom MassARRAY platform (Sequenom).

Techniques: DNA Methylation Assay

Journal: Oncotarget

Article Title: Candidate tumor suppressor ZNF154 suppresses invasion and metastasis in NPC by inhibiting the EMT via Wnt/β-catenin signalling

doi: 10.18632/oncotarget.20479

Figure Lengend Snippet: (A) CpG islands in ZNF154. The transcription start site (TSS) is indicated by a curved arrow. The regions analysed by methylation specific PCR (MSP) and MassARRAY are shown. (B) Relative ZNF154 expression in normal nasopharyngeal NP69 cells and NPC cell lines. Glyceraldehyde 3-phosphate dehydrogenase ( GAPDH ) was used as the endogenous control. (C) Relative ZNF154 expression in NPC tissues and non-cancer nasopharyngitis biopsy tissues (NCNBT). (D) Western blotting analysis of ZNF154 protein expression in NPC cell lines and NP69 cells. (E) Quantitative MassARRAY methylation analysis of ZNF154 in NP69 cell lines, normal tissues (NT), NPC cell lines and NPC tissue specimens (P). (F) Demethylation treatment with 5-Aza restored the expression of ZNF154 in NPC cell lines. (G) MSP analysis of the methylation status of ZNF154 after demethylation treatment of NPC cell lines; M, methylated allele; U, unmethylated allele.

Article Snippet: The methylation status of ZNF154 in NPC was detected with Methylation specific-PCR (MSP) and Quantitative Sequenom MassARRAY.

Techniques: Methylation, Expressing, Control, Western Blot

Journal: Oncotarget

Article Title: Candidate tumor suppressor ZNF154 suppresses invasion and metastasis in NPC by inhibiting the EMT via Wnt/β-catenin signalling

doi: 10.18632/oncotarget.20479

Figure Lengend Snippet: PCR primer sequences

Article Snippet: The methylation status of ZNF154 in NPC was detected with Methylation specific-PCR (MSP) and Quantitative Sequenom MassARRAY.

Techniques: Sequencing, Reverse Transcription, Methylation

Journal: European Journal of Human Genetics

Article Title: Human active X-specific DNA methylation events showing stability across time and tissues

doi: 10.1038/ejhg.2014.34

Figure Lengend Snippet: Sex-specific DNA methylation at the BCOR promoter and CpG islands. (a) Genomic regions showing clear differential methylation patterns between males and females in both tissues and time points. BCOR_1 and BCOR_2 denote regions where the methylation was also assessed by Sequenom EpiTYPER MassARRAY. (b) Differential methylation patterns between males and females detected by the HM450, *HM450 probe CpG sites that were also assessed by Sequenom EpiTYPER. (c) Differential methylation patterns of 12 placental tissue samples in two regions detected by EpiTYPER, the regions clearly show a sex-specific pattern. Error bars denote 95% confidence intervals.

Article Snippet: BCOR_1 and BCOR_2 denote regions where the methylation was also assessed by Sequenom EpiTYPER MassARRAY. ( b ) Differential methylation patterns between males and females detected by the HM450, *HM450 probe CpG sites that were also assessed by Sequenom EpiTYPER. ( c ) Differential methylation patterns of 12 placental tissue samples in two regions detected by EpiTYPER, the regions clearly show a sex-specific pattern.

Techniques: DNA Methylation Assay, Methylation