Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 1. Genomic coverage of the TruSeq EPIC at different sequencing depths for the 11 breast tissue samples. T, breast tumour tissue; AN, adjacent normal breast tissue; K, normal breast tissue.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Sequencing

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 2. The distribution of CpGs by different genomic annotations from TruSeq EPIC (≥10X) and EPIC-array platforms. (a) CpG- island context; (b) genomic function context; (c) regulatory region context; (d) chromosome.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques:

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 4. Pearson correlation between methylation β-values of the common CpGs across TruSeq EPIC (≥10X) and EPIC-array platforms by different sequencing depth for our 11 breast tissue samples.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Methylation, Sequencing

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 3. Distribution of methylation β values from the two platforms for our 11 breast tissue samples. (a) the common CpGs across the two platforms in TruSeq EPIC (≥10X); (b) the common CpGs in EPIC-array; (c) all CpGs detected in TruSeq EPIC (≥10X); (d) all CpG detected in EPIC-array.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Methylation

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 5. Scatterplots and Pearson correlations of the mean methylation β values for the common CpGs from TruSeq EPIC (≥10X) and EPIC-array data. Red dotted lines denote Y = X. (a) T samples; (b) AN samples; (c) K samples; (d) all samples combined.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Methylation

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 6. Scatterplots and Pearson correlations of the mean differences of methylation β values (∆β) for the common CpGs between two tissue types from TruSeq EPIC (≥10X) and EPIC-array data. Red dotted lines denote Y = X. (a) T vs. K; (b) T vs. AN; and (c) AN vs. K.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Methylation

Journal: Epigenetics

Article Title: Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray.

doi: 10.1080/15592294.2020.1827703

Figure Lengend Snippet: Figure 7. The number of differentially methylated positions (DMPs) between tissue types identified by TruSeq EPIC (≥10X) and EPIC- array platforms. DMPs were defined by FDR < 0.05 and |∆β| ≥ 0.1. (a) the common CpGs across the two platforms; (b) all CpGs detected by each platform.

Article Snippet: A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing.

Techniques: Methylation

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