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.