Additional file 2 of Exposing the DNA methylation-responsive compartment of the leukaemic genome in T-ALL cell lines support its potential as a novel therapeutic target in T-ALL

Additional file 2. Supplementary Table 1. Sequencing metrics for low pass whole methylome sequencing of untreated T-ALL cell lines. Supplementary Table 2. Average CpG methylation as percentage, globally and at specific genomic regions, assessed by low pass whole methylome sequencing of untreated T-ALL cell lines. Supplementary Table 3. Average coverage per CpG for low pass whole methylome sequencing of untreated T-ALL cell lines. Supplementary Table 4. Sequencing metrics for low pass whole methylome sequencing of ALL-SIL, LOUCY, JURKAT and SUP-T1 cells treated with increasing concentrations of 5-azacytidine (AZA), 5-aza-2′-deoxycytidine (DAC), and GSK-3685032 (GSK5032) for 3 and 7 days. Supplementary Table 5. Average CpG methylation as percentage, globally and at specific genomic regions, assessed by low pass whole methylome sequencing of ALL-SIL, LOUCY, JURKAT, and SUP-T1 cells treated with increasing concentrations of 5-azacytidine (AZA), 5-aza-2′-deoxycytidine (DAC), and GSK-3685032 (GSK5032) for 3 and 7 days. Supplementary Table 6. Average coverage per CpG for low pass whole methylome sequencing of ALL-SIL, LOUCY, JURKAT, and SUP-T1 cells treated with increasing concentrations of 5-azacytidine (AZA), 5-aza-2′-deoxycytidine (DAC), and GSK-3685032 (GSK5032) for 3 and 7 days. Supplementary Table 7. Sequencing metrics for Enzymatic Methyl-sequencing, deep sequencing, of LOUCY and SUP-T1 cells treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days or 300 nM GSK-3685032 (GSK5032) for 3 and 7 days. Supplementary Table 8. Differential methylation at promoters for LOUCY (L) and SUP-T1 (S) cells treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). DNA methylation on a scale from 0 to 1. q value, BH-corrected p-value. Supplementary Table 9. List of genes whose promoters show ≥ 80% DNA methylation in control cells (ctrl) or in cells treated with 300 nM GSK-3685032 (GSK5032) for 7 days (retain) in LOUCY and SUP-T1 cells. Supplementary Table 10. Gene ontology (GO) enrichment analysis for genes retaining DNA methylation at promoters in both LOUCY and SUP-T1 cells (overlap) and for methylation-sensitive genes in LOUCY and SUP-T1 cell individually after treatment with GSK-3685032 (GSK5032) for 7 days. Supplementary Table 11. Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis for genes retaining DNA methylation at promoters in both LOUCY and SUP-T1 cells (overlap) and for methylation-sensitive genes in LOUCY and SUP-T1 cell individually after treatment with GSK-3685032 (GSK5032) for 7 days. Supplementary Table 12. Differential gene expression promoters for LOUCY (L) and SUP-T1 (S) cells treated with 10 nM 5-aza-2′-deoxycytidine for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Supplementary Table 13. Differential methylation at promoters and corresponding gene expression for promoters for LOUCY (L) and SUP-T1 (S) cells treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Selected for curated, NM_* and NR_*, transcripts. Supplementary Table 14. Genes used for enrichment analyses. Supplementary Table 15. Differential methylation of transposable elements for LOUCY cells (L) treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Supplementary Table 16. Differential methylation of transposable elements for SUP-T1 cells (S) treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Supplementary Table 17. Differential expression of transposable elements for LOUCY cells (L) treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Supplementary Table 18. Differential expression of transposable elements for SUP-T1 cells (S) treated with 10 nM 5-aza-2′-deoxycytidine (DAC) for 3 days (D3) or 300 nM GSK-3685032 (GSK5032) for 3 (G3) and 7 days (G7). Supplementary Table 19. Genes used for the enrichment analysis of the molecular signature database datasets HALLMARK_INTERFERON_ALPHA_RESPONSE (M5911) and the CP:REACTOME dataset REACTOME_STING_MEDIATED_INDUCTION_OF_HOST_IMMUNE_RESPONSES (M27045), along with whether they were detected and differentially expressed in LOUCY and SUP-T1 cells treated with 300 nM GSK-3685032 for 7 days (G7). Supplementary Table 20. Overview of nucleoside and non-nucleoside compounds.

附加文件2。补充表1：未经处理的T细胞急性淋巴细胞白血病（T-cell Acute Lymphoblastic Leukemia, T-ALL）细胞系的低pass全甲基组测序（low pass whole methylome sequencing）测序质控指标。补充表2：未经处理的T-ALL细胞系经低pass全甲基组测序检测得到的全局及特定基因组区域的CpG平均甲基化水平（以百分比计）。补充表3：未经处理的T-ALL细胞系经低pass全甲基组测序得到的每个CpG位点的平均覆盖度。补充表4：经递增浓度的5-氮胞苷（5-azacytidine, AZA）、5-氮-2′-脱氧胞苷（5-aza-2′-deoxycytidine, DAC）及GSK-3685032（GSK5032）处理3天和7天后的ALL-SIL、LOUCY、JURKAT及SUP-T1细胞的低pass全甲基组测序测序质控指标。补充表5：经递增浓度的AZA、DAC及GSK5032处理3天和7天后的ALL-SIL、LOUCY、JURKAT及SUP-T1细胞经低pass全甲基组测序检测得到的全局及特定基因组区域的CpG平均甲基化水平（以百分比计）。补充表6：经递增浓度的AZA、DAC及GSK5032处理3天和7天后的ALL-SIL、LOUCY、JURKAT及SUP-T1细胞的低pass全甲基组测序每个CpG位点的平均覆盖度。补充表7：经10 nM 5-氮-2′-脱氧胞苷（DAC）处理3天，或经300 nM GSK5032处理3天、7天的LOUCY及SUP-T1细胞的酶促甲基化测序（Enzymatic Methyl-sequencing）深度测序质控指标。补充表8：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的LOUCY（L）及SUP-T1（S）细胞的启动子区域差异甲基化分析结果。DNA甲基化水平取值范围为0至1；q值为本雅明尼-霍赫贝格（BH）校正P值。补充表9：在LOUCY及SUP-T1细胞中，对照组（ctrl）或经300 nM GSK5032处理7天（G7）后其启动子区域DNA甲基化水平≥80%的基因列表（保留甲基化的基因）。补充表10：经GSK5032处理7天后，LOUCY与SUP-T1细胞中共有的启动子区域保留DNA甲基化的基因，以及两个细胞系各自的甲基化敏感基因的基因本体（Gene Ontology, GO）富集分析结果。补充表11：经GSK5032处理7天后，LOUCY与SUP-T1细胞中共有的启动子区域保留DNA甲基化的基因，以及两个细胞系各自的甲基化敏感基因的京都基因与基因组百科全书（Kyoto Encyclopaedia of Genes and Genomes, KEGG）富集分析结果。补充表12：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的LOUCY（L）及SUP-T1（S）细胞的启动子区域差异基因表达分析结果。补充表13：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的LOUCY（L）及SUP-T1（S）细胞的启动子区域差异甲基化及对应基因表达分析结果，仅筛选经注释的NM_*及NR_*转录本。补充表14：富集分析所用的基因列表。补充表15：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的LOUCY（L）细胞的转座元件差异甲基化分析结果。补充表16：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的SUP-T1（S）细胞的转座元件差异甲基化分析结果。补充表17：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的LOUCY（L）细胞的转座元件差异表达分析结果。补充表18：经10 nM DAC处理3天（D3），或经300 nM GSK5032处理3天（G3）、7天（G7）的SUP-T1（S）细胞的转座元件差异表达分析结果。补充表19：用于分子特征数据库（Molecular Signature Database, MSigDB）数据集HALLMARK_INTERFERON_ALPHA_RESPONSE（M5911）及CP:REACTOME数据集REACTOME_STING_MEDIATED_INDUCTION_OF_HOST_IMMUNE_RESPONSES（M27045）富集分析的基因列表，以及这些基因在经300 nM GSK5032处理7天（G7）的LOUCY及SUP-T1细胞中的检测情况与差异表达状态。补充表20：核苷类与非核苷类化合物概述。