Journal: International Journal of Molecular Sciences

Article Title: Effects and Mechanism of Particulate Matter on Tendon Healing Based on Integrated Analysis of DNA Methylation and RNA Sequencing Data in a Rat Model

doi: 10.3390/ijms23158170

Figure Lengend Snippet: ( A ) Kyoto Encyclopedia of Genes and Genome (KEGG) pathways associated with the significantly upregulated and downregulated differentially expressed genes (DEGs) between particulate matter (PM)-exposed and control (non-PM) rats ( p < 0.05). ( B ) Canonical pathways with significant Z-scores (>2) identified using ingenuity pathway analysis. Heatmaps showing the DEGs in the ( C ) cAMP response element-binding protein (CREB) and ( D ) cAMP signaling pathways. ( E ) Schematic diagram showing the methods and criteria for gene analysis. ( F ) Venn diagram showing the combined DNA methylation and transcriptome data. The red circle indicates 67 genes exhibiting hypomethylated/upregulated expression. ( G ) The top five KEGG pathways associated with the hypomethylated/upregulated genes.

Article Snippet: A DNA methylation microarray was performed by Genomictree (Daejeon, Korea) using the tendon tissues (n = 3 per group) and a custom-designed Agilent-based microarray platform with 2 × 400 K probes per slide (popular_2X400K_chip; Agilent Design ID: 086791; Agilent Technologies, Santa Clara, CA, USA).

Techniques: Control, Binding Assay, Protein-Protein interactions, DNA Methylation Assay, Expressing

Journal: Genes

Article Title: Epigenetic Heterogeneity of B-Cell Lymphoma: DNA Methylation, Gene Expression and Chromatin States

doi: 10.3390/genes6030812

Figure Lengend Snippet: DNA methylation summary characteristics of lymphoma and of healthy B and GCB cells. ( a ) The frequency distribution of the promoter methylation beta values of B-cells shows two maxima referring to almost not- and completely methylated promoters, respectively; The distributions of beta values loose this bimodality to a large degree in lymphoma where weakly and intermediately methylated genes become hyper-methylated and highly methylated genes become hypo-methylated compared with healthy B-cells ( b + c ); ( d ) The total methylation level increases and ( e ) the variability of methylation among the genes in each of the samples decreases.

Article Snippet: Microarray-derived DNA methylation data (GoldenGate Methylation Cancer Panel I; Illumina, San Diego, CA) of in total 133 samples obtained from hematological neoplasms and reference systems were taken from [ ] in terms of beta values of 1410 CpG’s located in the range of −1500 bp to +500 bp around the transcription start site of 768 genes thus serving as markers for their promoter methylation.

Techniques: DNA Methylation Assay, Methylation

Journal: Genes

Article Title: Epigenetic Heterogeneity of B-Cell Lymphoma: DNA Methylation, Gene Expression and Chromatin States

doi: 10.3390/genes6030812

Figure Lengend Snippet: SOM portraying of the DNA methylation landscape of lymphoma (MetSOM). ( a ) SOM portraits of histological lymphoma classes and of controls. Red and blue colors assign regions containing genes with high and low methylation levels, respectively; ( b ) the methylation overview map summarizes regions hypermethylated in any of the classes compared with any other one in red. The methylation variance map identifies regions of highly variable (red) and almost invariant (blue) beta values; ( c ) The methylation profiles show the mean methylation level among the samples of genes taken from the “spot” regions 1–6 assigned in the methylation overview map. Horizontal dashed lines serve as guide for the eye showing the mean methylation level of the respective spot averaged over all samples. Assignments as “hyper-” or “hypomethylated” refer to relative methylations compared with B-cells. Lists of genes in these regions are given in .

Article Snippet: Microarray-derived DNA methylation data (GoldenGate Methylation Cancer Panel I; Illumina, San Diego, CA) of in total 133 samples obtained from hematological neoplasms and reference systems were taken from [ ] in terms of beta values of 1410 CpG’s located in the range of −1500 bp to +500 bp around the transcription start site of 768 genes thus serving as markers for their promoter methylation.

Techniques: DNA Methylation Assay, Methylation