Journal: Cell Genomics

Article Title: A timely, user-friendly analysis of the mouse DNA methylome

doi: 10.1016/j.xgen.2022.100153

Figure Lengend Snippet: Analyzing mouse DNA methylation through a microarray Top: examples of the biological questions interrogated in Zhou et al. Bottom: an illustrative representation of CpG sites in the epigenomics platform and its user-friendly interface that allows for easy access to databases.

Article Snippet: The gold-standard platform is the EPIC Infinium DNA methylation microarray.

Techniques: DNA Methylation Assay, Microarray

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: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Venn diagram showing the degree of CpG overlapping (yellow) between the Infinium HumanMethylation450 BeadChip (450K; red) and the MethylationEPIC BeadChip (850K; green) microarrays.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques:

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Comparison of methylation values from HumanMethylation450 and their corresponding shared CpG sites present on MethylationEPIC microarray (A) for a renal tumor sample (RCC9). Assay reproducibility (B) of methylation measurements when using technical replicates on a normal colon (NC22A) sample. Correlation plot (C) of the methylation values obtained from a FFPE sample (RCC9-FFPE) when compared with its match biopsy of the same tumor that was preserved as FF (RCC9). 5-hmC value representation (D) , where the same sample was treated as per conventional bifsulfite conversion or as per oxBS. Differences on oxBS with bifsulfite conversion are due to the level of 5-hydroxymethylation, where the absence of 5-hmC has been modeled as a discontinue red line. Frequency of hydroxymethylaton values (E) as a result of subtracting the oxBS values (due to 5-mC) from the BS values (due to 5-mC + 5-hmC) for each CpG site included on the 850K array. 5-hmC: 5-hydroxymethylation; FF: Fresh frozen; FFPE: Formalin-fixed paraffin-embedded; oxBS: Oxidative bisulfite conversion.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Comparison, Methylation, Microarray, Formalin-fixed Paraffin-Embedded

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: (A) Differentially methylated CpG sites (Δβ ≥0.66 ) on MethylationEPIC BeadChip microarray from a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue. (B) Differentially methylated CpG sites (Δβ ≥0.66), among the newly added 413,759 CpG sites of the MethylationEPIC BeadChip microarray, for a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Methylation, Microarray