Additional file 2: Figure S1. of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

Cell type-specific DNA methylation. A) Bisulfite sequencing results of Hpa_1553647. Each row represents the sequence result from bisulfite PCR products. We show four amnion, four amniotic epithelial cell, and amniotic stromal cell results. The amniotic epithelial and stromal cells were isolated from four individuals. The blue arrow indicates the Hpa_1553647 position in the sequencing results. B) Bisulfite MassArray results of Hpa_210409 and Hpa_621984. The y-axis shows the % DNA methylation in amniotic epithelial and amniotic stromal cells (from four individuals). The p values were calculated by a t test. The error bars indicate the standard deviations. (PDF 317 kb

Additional file 3: Table S1. of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

Lists of p values of principal component analysis with known covariates. Table S2. A list of differentially expressed genes. Table S3. Lists of differentially methylated HpaII sites in each model. Table S4. A list of differentially methylated HpaII sites with previously reported Infinium HumanMethylation450 BeadChip differentially methylated probes. Table S5. A list of variably methylated HpaIIs. Table S6. A list of var-HpaII sites harboring genes. (XLSX 374 kb

Additional file 6: Figure S4. of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

Comparison of the DNA methylation distribution of variable HpaII sites. The distributions of the DNA methylation levels of variable methylation sites in severe PE-exposed (PE_S, green) (proteinuria grade ≥3 and systolic blood pressure ≥160 mmHg), less severe PE-exposed (PE_M, orange) (proteinuria grade ≤1 and systolic blood pressure ≥ 140 mmHg) and control (blue) were summarized graphically in violin plots. (PDF 895 kb

Additional file 7: of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

Codes used in this study. (TXT 66.7 kb

Comparative analysis of CRY1 expression in a panel of different lymphoid malignancies.

<p>qRT-PCR analyses of PBMC samples obtained from patients with T-prolymphocytic leukemia (T-PLL), mantle cell lymphoma (MCL), plasma cell leukemia (PCL), hairy cell leukemia (HCL), B and T cell acute lymphoblastic leukemia (B-ALL, T-ALL), CLL and normal donors (ND), A. Red characters indicate samples that were further subjected to DNA methylation analysis of the CRY1 promoter, A. Analysis of CRY1 CpG island promoter methylation status, B. For experimental details and description of the graph in panel B refer to the legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034347#pone-0034347-g002" target="_blank">Figure 2</a>.</p

Analysis of CRY1 CpG island promoter methylation status measured with the Bisulphite MassArray assay.

<p><b>A</b> Results of CRY1 CpG island methylation analysis performed on CLL samples and normal donors (ND) grouped by CD38 expression (CD38− samples, n = 28; CD38+ samples, n = 30; ND, n = 5). Each value represents the average amount of methylated CpGs of all analyzable CpGs within the CpG island promoter from one patient. The values represent the mean of duplicate experiments. The IgVH mutational status of each patient (if available) is highlighted in red; circles and squares indicate unmutated IgVH/V3-21 and mutated IgVH status, respectively. The median is marked as a line, error bars indicate SEM. Unpaired two-tailed t-test was used to compute p-values. <b>B</b> Samples from CLL patients and ND were subjected to both CRY1 mRNA expression and DNA methylation analysis with the bisulphite MassArray assay. mRNA expression values and percentage of methylated CpG were found to be highly correlated (r = −0.63, p<0.0001, Spearman correlation). The regression line in the plot was produced by linear regression analysis using promoter methylation as dependent and CRY1 mRNA expression as independent variable. <b>C</b> Correlation between the methylation data resulting from bisulphite genomic sequencing and the MassArray method showed high consistency (r = 0.86, p<0.0001, Spearman correlation).</p

Expression of CRY1 in CLL subgroups and normal donors.

<p><i>CRY1</i> mRNA expression in normal donors (ND, n = 35) in comparison to CLL samples from prognostic subgroups defined by CD38 expression (A, CD38+ samples, n = 36 vs. CD38− samples, n = 39) and IgVH mutational status (B, IgVH unmutated/V3-21, UM/V3-21, n = 23 vs. IgVH mutated, M, n = 18). mRNA levels are relative to GAPDH. Data are presented in a box-and-whisker format: the difference of the 25th and 75th percentile form the box (interquartile range, IQR), with the median marked as a line; the whiskers go down to the smallest value and up to the largest values. The Mann-Whitney U-test was used to compute p-values for pairwise comparisons.</p

Treatment-free survival according to the methylation status of the CRY1 promoter region.

<p>Treatment-free survival of 53 CLL patients with lowly methylated (n = 26) and highly methylated (n = 27) CRY1 promoter.</p

Patient characteristics.

*<p>n.a., not available.</p

ATAC-seq sequencing data metrics for the human and <i>T</i>. <i>gondii</i> genomes.

(XLSX)</p