mouse methylation controls  (EpigenDx)

Journal: Journal of the American Heart Association

Article Title: DNA Methyltransferase 1–Dependent DNA Hypermethylation Constrains Arteriogenesis by Augmenting Shear Stress Set Point

doi: 10.1161/jaha.117.007673

Figure Lengend Snippet: Figure 2. Endothelial cells exposed to a nonreversed increase in shear stress magnitude exhibit augmented DNA methyltransferase 1 (DNMT1) expression and altered genome-wide DNA methylation patterns in vitro. A, Schematic depicting biomimetic shear stress conditions applied to human umbilical vein endothelial cells to simulate nonreversed/muscular (N, blue) and reversed/saphenous (R, orange) regions. B, Bar graph of DNMT1 mRNA expression in each flow condition 1 hour or 6 hours after simulated femoral artery ligation (FAL) (n=8 for 1 hour and n=6 for 6 hours). *P<0.05 between reversed and nonreversed within a time point, Student t test. Data are meanSEM. C through D, Scatter plot and Volcano plot of all differentially methylated regions in a gene promoter region (17 227 total). Significant differentially methylated regions were designated as hypomethylated (blue, 213 total) or hypermethylated (red, 603 total) with respect to the nonreversed condition (Table S3). E through F, Using our mRNA-sequencing data set, we further filtered this list of significantly hypermethylated and hypomethylated genes (816 total genes) to contain only those with gene expression changes between nonreversed and reversed conditions in the expected direction based on their change in promoter methylation, ie, genes that were downregulated and had a hypermethylated promoter (red, 250 genes) or were upregulated and had a hypomethylated promoter (blue, 127 genes) in nonreversed vs reversed conditions (Tables S4 and S5). FDR indicates false discovery rate.

Article Snippet: Differences in DNA methylation as detected by HRM were quantified by the net temperature shift as previously calculated.28 Briefly, the net temperature shift was calculated as average distance between the normalized melt curves of experimental samples from a universal methylated positive control (#D5012; Zymo Research) where a more negative net temperature shift indicates a less methylated sample.

Techniques: Shear, Expressing, Genome Wide, DNA Methylation Assay, In Vitro, Ligation, Methylation, Sequencing, Gene Expression

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) Workflow of designing the mouse Infinium methylation BeadChip. (B) The number of probes associated with each gene model biotype. (C) Enrichment of the probes in different chromatin states. The consensus chromatin states from 66 ENCODE ChromHMM files for twelve tissues were used. Distribution of interrogated CpGs in different chromatin states is shown at bottom left. (D) Heatmap representing unsupervised clustering of four intestinal tumor samples, each analyzed in 8-fold replicate, including at two separate laboratory facilities. 21,643 most variable probes are shown. (E and F) Smooth scatterplot of two replicates from Apc Min (E) or Mlh1 (F) tumor samples. The colors represent DNA methylation β values, and the β value difference between the two replicates is shown on the top right quadrant. (G) Probe success rate of samples of DNA input ranging from 5 to 1,000 ng. Data from two labs are represented by different shapes. (H) Smooth scatterplots contrasting the comparison of a low-input sample (5 ng) and a high-input sample (500 ng), both with 1,000-ng-input sample. Samples are losing intermediate methylation reading as DNA input decreases. (I) Reproducibility of DNA methylation measurement from four tissues comparing fresh frozen samples and samples fixed with formalin for 24 and 48 h. See also and ; .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: Methylation, DNA Methylation Assay

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) DNA methylation β value distribution of titration samples run from two different labs. (B) Comparison of median DNA methylation β values measured from the Infinium Mouse Methylation MM285 BeadChip (y axis) with titration fraction of methylated DNA (x axis). Two different labs are shown in different colors. (C) Comparison of DNA methylation β values measured from the MM285 array (y axis) with WGBS methylation level measurement on the mouse B16 melanoma cell line (45X mean CpG coverage) (x axis). (D) Methylation level distribution of J1 embryonic stem cells with different Dnmt1 genotypes. (E) Methylation level distribution of colon and testis DNA from Dnmt1 hypomorphic mice. (F) Methylation level distribution of 10T1/2 cells treated with decitabine (DAC) at 200 nM, or mock-treated with PBS solvent for 24 h and then sampled 12 and 24 days after treatment. See also and .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: DNA Methylation Assay, Titration, Methylation

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) Genomic distribution of DNA methylation level centered on CTCF binding sites and protein-coding genes (autosomal and X-linked). The CpG density per bp (top row), the designed probe density per bp (middle row), and the average methylation level of samples stratified by tissue type (bottom row) are shown accordingly. (B) Methylation level distribution of X-linked CpG-island CpGs in colon samples from male and female mice and testis samples from male mice. (C) Genomic distribution of X-linked CpGs (top), mouse MM285 probe density (middle), and the sex-specific methylation difference, represented by the slope of the sex-specific effect in a multiple regression (bottom). (D) Heatmap showing methylation level of CpGs (rows) associated with 13 curated imprinting control regions (ICRs) in non-malignant and intestinal tumor tissue samples (columns). CpGs are sorted by genomic coordinates. The associated ICR regions are labeled on the right. The grayscale horizontal bar on top represents Dnmt1 genotype and malignancy state. The second bar represents tissue type, using the color key as indicated above the left side of the heatmap. The third bar represents mouse age with the color key indicated on the right. (E) DNA methylation level distribution of CpGs associated with ICRs or secondary differentially methylated regions. Colon (left) and testis (right) samples from mouse samples of two sexes and Dnmt1 genotypes are shown. (F) Correlation with age of CpG DNA methylation levels at 13 ICRs in 128 colon and small intestine tissue samples. (G) Distribution of mitochondrial CpG methylation in colon and testis samples of different sex and Dnmt1 genotype. (H) Heatmap showing CpH methylation level. Rows correspond to cytosine loci in CpA, CpC, and CpT context. Columns correspond to ESCs and different tissue samples. See also ; and .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: DNA Methylation Assay, Binding Assay, Methylation, Labeling, CpG Methylation Assay

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: DNA Methylation Assay, Recombinant, Methylation, Software, Binding Assay, Modification

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) t-SNE cluster map showing samples clustered by tissue type (left) and sex (right). The color legend is the same as in . (B) Four-way Venn diagram showing CpGs differentially methylated with respect to strain, tissue, sex, and age in 467 mouse samples. (C) CpGs (rows) specifically methylated (top) and unmethylated (bottom) in each tissue (columns showing samples organized by tissue type). (D) CpGs (rows) specifically methylated (top) and unmethylated (bottom) in each sorted leukocyte cell type (columns showing samples organized by cell type). (E) Track view of the DNA methylation profile of the Mir200c locus as a marker for epithelial versus mesenchymal cells. Tissue type and mean methylation level of five CpGs associated with the Mir200c locus (shown by the red bar at the bottom) are shown on the right-hand side of the heatmap. (F) t-SNE cluster map of primary tissue samples from wild-type and Dnmt1 NR mice using tissue-specific hypomethylation (left) and hypermethylation signature (right). The color legend is the same as in . See also .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: Methylation, DNA Methylation Assay, Marker

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) Heatmap displaying DNA methylation gain associated with aging (top) and with tumorigenesis (bottom). Rows correspond to CpGs and columns correspond to samples. Left-hand side bar represents whether probes (rows) fall to CpG islands (CGI), Polycomb repressive complex group (PcG) target, and enhancer elements in small intestine samples. (B) Transcription factors whose binding sites are enriched in CpGs that gain methylation with age. y axis represents odds ratio of enrichment, and x axis represents number of significant probes overlapping binding sites. Size of the dots denotes statistical significance of the enrichment (Fisher’s exact test). (C) Transcription factors whose binding sites are enriched in CpGs that lose methylation with age. (D) Transcription factors whose binding sites are enriched in CpGs that gain methylation associated with tumorigenesis. Each dot corresponds to a transcription factor. (E) Ontology terms enriched in target genes regulated by enhancers that gain DNA methylation. (F) Transcription factors whose binding sites are enriched in CpGs that lose methylation associated with tumorigenesis. (G) Scatterplot comparing age predicted by a mouse epigenetic clock using 347 CpG probes (y axis) and reported age (x axis) in disease-free tissues. (H) Scatterplot comparing age predicted by a mouse epigenetic clock using 347 CpG probes (y axis) and reported age (x axis) in mouse intestinal tumors. See also and .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: DNA Methylation Assay, Binding Assay, Methylation

Journal: Cell genomics

Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

doi: 10.1016/j.xgen.2022.100144

Figure Lengend Snippet: (A) The numbers of functional EPIC and MM285 array probes on different vertebrate and invertebrate species. (B) Distribution of the DNA methylation reading of functional probes in the rat genome. Rat DNA samples were derived from mixing fully methylated and fully unmethylated rat DNA using titration ratios from 0% to 100%. (C) Probe success rates of the mouse (left) and EPIC arrays (right) on human-mouse mixture titrated at a range of percentages of the mouse DNA (x axis). Curves of different color represent probe sets that work on either both species (yellow) or only the designed species. (D) Principal component analysis showing the leading PC (PC1) on the x axis and combined PC2–10 on the y axis. Samples are colored by tissue with symbol shape representing species. (E and F) Heatmap display of the DNA methylation level of species-specific probes (E) and tissue-specific probes (F). (G) Cross-validation of estimating human DNA fraction using human-mouse variant probes (x axis) and using human-mouse non-syntenic probes from both mouse and EPIC arrays. Each triangle represents a human-mouse titration sample. Each circle represents a PDX sample. Color of the triangle corresponds to the known titration fraction of human DNA. See also ; and .

Article Snippet: Mouse DNA methylation calibration standards , EpigenDx , Cat# 80–8060M-PreMix.

Techniques: Functional Assay, DNA Methylation Assay, Derivative Assay, Methylation, Titration, Variant Assay