Journal: Clinical Epigenetics

Article Title: DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations

doi: 10.1186/s13148-015-0112-2

Figure Lengend Snippet: Volcano plots of the Illumina 27K data showing pairwise comparisons of Turner and Klinefelter samples to male and female samples. The differences in beta values between the respective comparisons is on the X-axis, while the –log10 ( p values) is on the Y-axis. Vertical dashed red/green and horizontal blue lines represent the 10 % methylation differences and the 5 % false discovery rates cutoff, respectively. The differentially methylated autosomal CpGs (>10 % differences and FDR <5 %) are represented by red and green filled circles for hypo and hyper methylated loci respectively; their corresponding number is also shown. The verified CpGs by pyrosequencing are represented as blue triangles (1 = cg2487174, 2 = cg16848873, 3 = cg24169822, 4 = cg11418559, 5 = cg20191453, 6 = cg09697795, 7 = cg18059933, 8 = cg26306976, 9 = cg04451770, 10 = cg06812844, 11 = cg04452095; loci labels are as in Fig. ). Cross-reactive loci, as defined by Chen Y. et al, are labeled with a black “x”. The numbers in each figure correspond to the number of individual CpG sites on autosomes that are hypomethylated ( left ) and hypermethylated ( right ); below each number ( in parenthesis ) is the corresponding number of differentially methylated CpG cites on the X chromosome

Article Snippet: Fig. 6 Trend in methylation differences at X chromosome between 46,XX and 47,XXY. a MeDIP data of the X chromosome in all four groups; all data are aligned to the transcription start site (TSS): 7 kb upstream and 3 kb downstream. b Illumina 27K methylation values; the data are divided into 10 pins depending on the degree of X inactivation of the corresponding locus (according to Carrel and Willard [ ]); average methylation at each pin is represented in the plot and the significant p value between female and Klinefelter samples at 0/9 is shown; all other comparisons between either female and Klinefelter or between male and Turners were not significant. c Detailed pyrosequencing data on two X-linked loci ( TEF3 and SLC35A2 ) showing the differences in average methylation between female and Klinefelter samples Fig. 7 Methylation at PAR regions. a MeDIP-based data.

Techniques: Methylation, Labeling

Journal: Clinical Epigenetics

Article Title: DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations

doi: 10.1186/s13148-015-0112-2

Figure Lengend Snippet: Trend in methylation differences at X chromosome between 46,XX and 47,XXY. a MeDIP data of the X chromosome in all four groups; all data are aligned to the transcription start site (TSS): 7 kb upstream and 3 kb downstream. b Illumina 27K methylation values; the data are divided into 10 pins depending on the degree of X inactivation of the corresponding locus (according to Carrel and Willard ); average methylation at each pin is represented in the plot and the significant p value between female and Klinefelter samples at 0/9 is shown; all other comparisons between either female and Klinefelter or between male and Turners were not significant. c Detailed pyrosequencing data on two X-linked loci ( TEF3 and SLC35A2 ) showing the differences in average methylation between female and Klinefelter samples

Article Snippet: Fig. 6 Trend in methylation differences at X chromosome between 46,XX and 47,XXY. a MeDIP data of the X chromosome in all four groups; all data are aligned to the transcription start site (TSS): 7 kb upstream and 3 kb downstream. b Illumina 27K methylation values; the data are divided into 10 pins depending on the degree of X inactivation of the corresponding locus (according to Carrel and Willard [ ]); average methylation at each pin is represented in the plot and the significant p value between female and Klinefelter samples at 0/9 is shown; all other comparisons between either female and Klinefelter or between male and Turners were not significant. c Detailed pyrosequencing data on two X-linked loci ( TEF3 and SLC35A2 ) showing the differences in average methylation between female and Klinefelter samples Fig. 7 Methylation at PAR regions. a MeDIP-based data.

Techniques: Methylation, Methylated DNA Immunoprecipitation

Journal: Clinical Epigenetics

Article Title: DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations

doi: 10.1186/s13148-015-0112-2

Figure Lengend Snippet: Hierarchical clustering and principal component analysis (PCA) of the Illumina 27K data. The figure is based only on autosomal loci. a Supervised analysis testing for differences between groups using ANOVA and applying a cutoff of <5 % false discovery rate (FDR), corresponding to a p value of 3.11E-4 and 148 CpG sites; b Unsupervised hierarchical clustering on the normalized data without applying a statistical hypothesis. The heat maps in the upper part of the figure correspond to one sample for each column and one locus for each horizontal line; red to green corresponds to relatively hypermethylated ( red ) to hypomethylated ( green ). In the lower part of the figure, each of the spheres corresponds to one sample and the connecting lines correspond to the two nearest neighbors (more similar) of a particular sample

Article Snippet: Fig. 6 Trend in methylation differences at X chromosome between 46,XX and 47,XXY. a MeDIP data of the X chromosome in all four groups; all data are aligned to the transcription start site (TSS): 7 kb upstream and 3 kb downstream. b Illumina 27K methylation values; the data are divided into 10 pins depending on the degree of X inactivation of the corresponding locus (according to Carrel and Willard [ ]); average methylation at each pin is represented in the plot and the significant p value between female and Klinefelter samples at 0/9 is shown; all other comparisons between either female and Klinefelter or between male and Turners were not significant. c Detailed pyrosequencing data on two X-linked loci ( TEF3 and SLC35A2 ) showing the differences in average methylation between female and Klinefelter samples Fig. 7 Methylation at PAR regions. a MeDIP-based data.

Techniques:

Journal: Epigenetics

Article Title: Prenatal medication exposure and epigenetic outcomes: a systematic literature review and recommendations for prenatal pharmacoepigenetic studies

doi: 10.1080/15592294.2021.1903376

Figure Lengend Snippet: Overview of the methodology and statistical analysis

Article Snippet: Combined epigenome-wide and candidate gene studies , Gurnot et al . (2015) [ ] , Cord blood , Genome-wide Site-by-site Gene-specific CYP2E1 both individual sites (16 CpGs) and global methylation , Genome-wide Infinium Human-Methylation27 BeadChip array (Illumina) Gene-specific PyroMark Q96 ID pyrosequencer (Qiagen) , Genome-wide β values Gene-specific Methylation percentage , Genome-wide Non-parametric Wilcoxon tests and linear regression models Gene-specific Linear regression models , FDR cut-off < 0.05 , 0 , No , The authors propose an epigenetic mediation mechanism based on three observations, suggesting that the DNAm of CYP2E1 is an epigenetic mechanism to protect the unborn child from the adverse effects of SRIs.

Techniques: Cell Counting, Transformation Assay, Methylation, Genome Wide, Functional Assay