Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem OxBS Illumina microarrays. Supplementary data

Name: Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem OxBS Illumina microarrays. Supplementary data
Creator: Taylor & Francis
Published: 2024-05-16 10:12:59
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DataCite Commons2024-05-16 更新2025-04-15 收录

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Table 1. Multivariable linear regression model outputs for comparing DNA extraction kit performance between BS and oxBS treated samples, with sample source adjusted. Table 2. Linear mixed effect model outputs for comparing DNA extraction kit performance between BS and oxBS treated samples, with sample source included as a random intercept. Table 3. Pairwise Wilcoxon rank sum test p-values from comparing the internal normalization control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted ccRCC samples. Figure 1. The probe call rate difference across all data sets Figure 2. Principal component regression analysis of technical variables in ccRCC samples Figure 3. Coefficient of variation and ICC in replicate human fetal oligodendrocyte samples. Figure 4. The recommended 5hmC cut-off batch 1 samples batch 2 samples using oxBSQC. Figure 5. The distribution of 5hmC signal in low-quality probe vs high quality probe in batch 1 samples batch 2 samples using oxBSQC. Figure 6. The CpG genomic location enrichment for low-quality probes in batch1 and batch2 using oxBSQC. Figure 7. The distribution of internal normalization control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted ccRCC samples

表1. 经样本来源校正后，用于比较亚硫酸氢盐（BS, Bisulfite）与氧化亚硫酸氢盐（oxBS, Oxidized Bisulfite）处理样本间DNA提取试剂盒性能的多变量线性回归模型输出结果。 表2. 以样本来源作为随机截距项，用于比较BS与oxBS处理样本间DNA提取试剂盒性能的线性混合效应模型输出结果。 表3. 比较BS转化与oxBS转化透明细胞肾细胞癌（ccRCC, clear cell renal cell carcinoma）样本中内部归一化对照探针（NORM_A/G/C/T）信号强度的两两Wilcoxon秩和检验P值。 图1. 全数据集探针检出率差异 图2. 透明细胞肾细胞癌样本中技术变量的主成分回归分析 图3. 重复人胎少突胶质细胞样本的变异系数与组内相关系数（ICC, Intraclass Correlation Coefficient） 图4. 基于oxBSQC工具为批次1、批次2样本推荐的5-羟甲基胞嘧啶（5hmC, 5-hydroxymethylcytosine）截断阈值 图5. 基于oxBSQC工具，批次1与批次2样本中低质量探针与高质量探针的5-羟甲基胞嘧啶信号分布情况 图6. 基于oxBSQC工具，批次1与批次2样本中低质量探针的CpG基因组区域富集特征 图7. BS转化与oxBS转化透明细胞肾细胞癌样本中内部归一化对照探针（NORM_A/G/C/T）的信号强度分布

提供机构：

Taylor & Francis

创建时间：

2022-05-03