Journal: iScience

Article Title: Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer

doi: 10.1016/j.isci.2024.109414

Figure Lengend Snippet: Global DNA methylation is altered at each stage of PDAC (A) Experimental design. Created with BioRender.com . FNA, Fine needle aspiration. (B) Principal component analysis (PCA) of WGBS data from mouse organoids. (C) Density plot of smoothed single CpG methylation values from mouse organoids. (D) PCA of WGBS data from patient-derived organoids (PDOs). (E) Density plot of smoothed single CpG methylation values from PDOs.

Article Snippet: WBGS sequencing libraries were constructed from 50 ng of converted DNA per sample using the TruSeq DNA Methylation Kit (Illumina).

Techniques: DNA Methylation Assay, CpG Methylation Assay, Derivative Assay

Journal: iScience

Article Title: Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer

doi: 10.1016/j.isci.2024.109414

Figure Lengend Snippet: DMR analysis of mouse organoids identifies a distinct DNA methylation signature in metastatic organoids (A) Heatmap of 20,392 significant (q < 0.01) DMRs from mN/mP versus mM comparison. (B) Heatmap of 4,116 significant (q < 0.01) DMRs from mT versus mM comparison. (C) Euler diagram of sequence overlaps for DMRs. (D and E) Top 10 KEGG and GO enrichments for (D) mN/mP versus mM DMRs and (E) mT versus mM DMRs. (F and G) Top 10 transcription factor motif enrichments for (F) mN/mP versus mM DMRs and (G) mT versus mM DMRs.

Article Snippet: WBGS sequencing libraries were constructed from 50 ng of converted DNA per sample using the TruSeq DNA Methylation Kit (Illumina).

Techniques: DNA Methylation Assay, Comparison, Sequencing

Journal: iScience

Article Title: Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer

doi: 10.1016/j.isci.2024.109414

Figure Lengend Snippet: DMR analysis of PDOs identifies a DNA methylation signature associated with late-stage disease (A) Heatmap of 5,374 significant (q < 0.05) DMRs for early- versus late-stage organoid comparison. (B) Top 10 KEGG and GO enrichments for early- versus late-stage DMRs. (C) Top 10 transcription factor motif enrichments for DMRs hypomethylated in late-stage organoids.

Article Snippet: WBGS sequencing libraries were constructed from 50 ng of converted DNA per sample using the TruSeq DNA Methylation Kit (Illumina).

Techniques: DNA Methylation Assay, Comparison

Journal: iScience

Article Title: Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer

doi: 10.1016/j.isci.2024.109414

Figure Lengend Snippet: DNA methylation correlates with gene expression changes that have prognostic value (A) Percent of DMRs with correlations between DNA methylation and gene expression. RNA-seq of mT and mM organoids ( GSE142467 ) and RNA-seq of early-stage and late-stage organoids. (B) Distribution of gene region annotations in DMRs where DNA methylation levels correlate with expression of the associated gene for mT versus mM DMRs and early- versus late-stage DMRs. (C and D) Low methylation in late-stage organoids (left graph) and positive correlation between DNA methylation and normalized gene expression (right graph) in DMRs associated with glutamatergic synapse-related genes: (C) DLGAP1 and (D) SH3GL2. Normalized gene expression calculated with DESeq2. (E and F) Kaplan-Meier survival showing poor survival in patients with low mRNA expression of (E) DLGAP1 and (F) SH3GL2 in TCGA-PAAD data.

Article Snippet: WBGS sequencing libraries were constructed from 50 ng of converted DNA per sample using the TruSeq DNA Methylation Kit (Illumina).

Techniques: DNA Methylation Assay, Gene Expression, RNA Sequencing, Expressing, Methylation

Journal: Clinical Epigenetics

Article Title: Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements

doi: 10.1186/s13148-021-01121-6

Figure Lengend Snippet: Methylation status at the promoter region of 32 escape genes examined by array-based methylation analysis using the Illumina Infinium Human Methylation EPIC BeadChip kit in the four patients. The heat map of β values in the four patients. The probes with lower than 0.25 in the β value are shown in gray and those with higher methylation (over 0.25) are shown in pink. The names of escape genes are shown at the right side of the heat map. The names of the three genes with abnormal methylation in Patient 1 are exhibited in red. The number of probes in each gene is shown as the height of each gene in the heat map (the height of one probe and two probes is exemplified at the lower right part of the figure)

Article Snippet: We subjected bisulfite-treated gDNA to the Illumina Infinium Human Methylation EPIC BeadChip (Illumina) and scanned by the Illumina iScan system.

Techniques: Methylation