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Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. <t>DNA</t> methylation was detected in SCLC tumors and adjacent normal tissues <t>(FFPE</t> 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.
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Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. <t>DNA</t> methylation was detected in SCLC tumors and adjacent normal tissues <t>(FFPE</t> 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.
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Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. <t>DNA</t> methylation was detected in SCLC tumors and adjacent normal tissues <t>(FFPE</t> 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.
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Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. <t>DNA</t> methylation was detected in SCLC tumors and adjacent normal tissues <t>(FFPE</t> 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.
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Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. <t>DNA</t> methylation was detected in SCLC tumors and adjacent normal tissues <t>(FFPE</t> 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.
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Image Search Results


Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. DNA methylation was detected in SCLC tumors and adjacent normal tissues (FFPE 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.

Journal: iScience

Article Title: Cisplatin resistance-related transcriptome and methylome integration identifies PCDHB4 as a novel prognostic biomarker in small cell lung cancer.

doi: 10.1016/j.isci.2024.110413

Figure Lengend Snippet: Figure 5. The validation of hypomethylation of the PCDHB4 gene in SCLC specimens by MeDIP-seq and BSP (A) Volcano plot of differentially methylated sites between SCLC tumors and adjacent normal tissues by MeDIP-seq. (B) The proportion of differentially methylated sites in all detected methylated sites. (C) The category of genomic locations for hypermethylated or hypomethylated sites. (D) GO analysis for the differentially methylation genes. Top 10 terms are shown. Neuron-associated pathways are marked in red. (E) Bar plot of GSEA based on the differentially methylation genes. (F) Boxplot showing the methylation level within the PCDHB4 promoter in SCLC tumors and adjacent normal tissues. (G) Distribution of differentially methylated sites on chromosomes. The red area represents the hypermethylated region, and the blue area represents the hypomethylated region. The PCDHB4 gene locates in the orange box. (H) The peak maps of methylation with PCDHB4 promoter by MeDIP-seq. DNA methylation was detected in SCLC tumors and adjacent normal tissues (FFPE 1, FFPE 2, FFPE 3, and FFPE 4) by MeDIP-seq. cfDNA methylation of an SCLC patient (before treatment and after recurrence) was detected by MeDIP-seq. (I) BSP analysis of the CpG site cg24918705 in SCLC tumor and adjacent normal tissue.

Article Snippet: DH5a TOLOBIO Cat# CC96102-02 pClone007 Simple Vector TsingKe Biotech Cat# TSV-007S Biological samples FFPE samples of human SCLC and adjacent non-tumor tissues The First Affiliated Hospital of USTC (Hefei, China) N/A Blood samples of SCLC patients The First Affiliated Hospital of USTC (Hefei, China) N/A Chemicals, peptides, and recombinant proteins RPMI-1640 Gibco Cat# 11875500BT Fetal bovine serum ExCell Bio Cat# FSP500 Penicillin-streptomycin solution Hyclone Cat# SV30010 Cisplatin MCE Cat# HY-17394 Critical commercial assays GeneRead DNA FFPE Kit Qiagen Cat# 180134 Circulating Nucleic Acids Kit Qiagen Cat# 55114 DNA Methylation kit Zymo Research Cat# D5001 RNA extraction kit Tiangen Cat# DP451 Reverse transcription kit TransGen Cat# AT301-03 BCA Protein Assay Kit Beyotime Cat# P0009 NEBNext Multiplex Oligos for Illumina New England BioLabs Cat# E7335L KAPA HiFi Hotstart ReadyMix KAPA Biosystems Cat# KK2602 KAPA HyperPrep Kit KAPA Biosystems Cat# KK8504 MagMeDIP Kit Diagenode Cat# C02010021 HighGene transfection reagent ABclonal Technology Cat# RM09014 CellTiter-Glo Luminescent Cell Viability assay Promega Cat# G7572

Techniques: Biomarker Discovery, Methylated DNA Immunoprecipitation, Methylation, DNA Methylation Assay