ERX1299522 E-MTAB-4341:BMA ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043386 SAMEA3856252 E-MTAB-4341:BMA BMA Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: none disease ERX1299523 E-MTAB-4341:BMB ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043387 SAMEA3856253 E-MTAB-4341:BMB BMB Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: none disease ERX1299524 E-MTAB-4341:NPB1 ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043388 SAMEA3856254 E-MTAB-4341:NPB1 NPB1 Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: none disease ERX1299525 E-MTAB-4341:NPB2 ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043389 SAMEA3856255 E-MTAB-4341:NPB2 NPB2 Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: none disease ERX1299526 E-MTAB-4341:NPB3 ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043390 SAMEA3856256 E-MTAB-4341:NPB3 NPB3 Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: none disease ERX1299527 E-MTAB-4341:P10_AP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043391 SAMEA3856257 E-MTAB-4341:P10_AP P10_AP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: accelerated phase chronic myeloid leukemia disease staging ERX1299528 E-MTAB-4341:P11_AP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043392 SAMEA3856258 E-MTAB-4341:P11_AP P11_AP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: accelerated phase chronic myeloid leukemia disease staging ERX1299529 E-MTAB-4341:P12_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043393 SAMEA3856259 E-MTAB-4341:P12_BC P12_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299530 E-MTAB-4341:P13_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043394 SAMEA3856260 E-MTAB-4341:P13_BC P13_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299531 E-MTAB-4341:P14_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043395 SAMEA3856261 E-MTAB-4341:P14_CP P14_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299532 E-MTAB-4341:P15_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043396 SAMEA3856262 E-MTAB-4341:P15_CP P15_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299533 E-MTAB-4341:P16_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043397 SAMEA3856263 E-MTAB-4341:P16_CP P16_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299534 E-MTAB-4341:P17_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043398 SAMEA3856264 E-MTAB-4341:P17_CP P17_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299535 E-MTAB-4341:P18_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043399 SAMEA3856265 E-MTAB-4341:P18_CP P18_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299536 E-MTAB-4341:P19_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043400 SAMEA3856266 E-MTAB-4341:P19_CP P19_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299537 E-MTAB-4341:P1_AP_BM ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043401 SAMEA3856267 E-MTAB-4341:P1_AP_BM P1_AP_BM Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: accelerated phase chronic myeloid leukemia disease staging ERX1299538 E-MTAB-4341:P1_AP_PB ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043402 SAMEA3856268 E-MTAB-4341:P1_AP_PB P1_AP_PB Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: accelerated phase chronic myeloid leukemia disease staging ERX1299539 E-MTAB-4341:P1_CP1_PB ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043403 SAMEA3856269 E-MTAB-4341:P1_CP1_PB P1_CP1_PB Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299540 E-MTAB-4341:P1_CP2_PB ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043404 SAMEA3856270 E-MTAB-4341:P1_CP2_PB P1_CP2_PB Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299541 E-MTAB-4341:P1_CP_BM ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043405 SAMEA3856271 E-MTAB-4341:P1_CP_BM P1_CP_BM Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299542 E-MTAB-4341:P20_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043406 SAMEA3856272 E-MTAB-4341:P20_CP P20_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299543 E-MTAB-4341:P21_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043407 SAMEA3856273 E-MTAB-4341:P21_CP P21_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299544 E-MTAB-4341:P22_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043408 SAMEA3856274 E-MTAB-4341:P22_CP P22_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299545 E-MTAB-4341:P23_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043409 SAMEA3856275 E-MTAB-4341:P23_CP P23_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299546 E-MTAB-4341:P2_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043410 SAMEA3856276 E-MTAB-4341:P2_BC P2_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299547 E-MTAB-4341:P2_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043411 SAMEA3856277 E-MTAB-4341:P2_CP P2_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299548 E-MTAB-4341:P3_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043412 SAMEA3856278 E-MTAB-4341:P3_BC P3_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299549 E-MTAB-4341:P3_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043413 SAMEA3856279 E-MTAB-4341:P3_CP P3_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299550 E-MTAB-4341:P4_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043414 SAMEA3856280 E-MTAB-4341:P4_BC P4_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299551 E-MTAB-4341:P4_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043415 SAMEA3856281 E-MTAB-4341:P4_CP P4_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299552 E-MTAB-4341:P5_BC_BM ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043416 SAMEA3856282 E-MTAB-4341:P5_BC_BM P5_BC_BM Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299553 E-MTAB-4341:P5_BC_PB ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043417 SAMEA3856283 E-MTAB-4341:P5_BC_PB P5_BC_PB Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299554 E-MTAB-4341:P6_CP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043418 SAMEA3856284 E-MTAB-4341:P6_CP P6_CP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: chronic phase chronic myeloid leukemia disease staging ERX1299555 E-MTAB-4341:P7_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043419 SAMEA3856285 E-MTAB-4341:P7_BC P7_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299556 E-MTAB-4341:P8_BC ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043420 SAMEA3856286 E-MTAB-4341:P8_BC P8_BC Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: blast crisis chronic myeloid leukemia disease staging ERX1299557 E-MTAB-4341:P9_AP ERP014005 E-MTAB-4341 Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples ERS1043421 SAMEA3856287 E-MTAB-4341:P9_AP P9_AP Bisulfite-Seq GENOMIC Reduced Representation Mononuclear cells were isolated from peripheral blood or bone marrow using Ficoll. Genomic DNA (gDNA) was isolated from MNCs using QIAsymphony DSP DNA Midi Kit (Qiagen), MspI (New England Biolabs, NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) and dATP, dCTP and dGTP. Illumina adapters were ligated using Quick Ligase (NEB) followed by AMPure XP bead size selection (Beckman Coulter). RRBS libraries were bisulfite treated using EZ DNA MethylationDirect kit (Zymo Research) followed by quantification by qPCR. Enrichment PCR was performed using PfuTurbo Cx Hotstart kit (Agilent Technologies) followed by AMPure XP bead clean up. Quality of final libraries was checked by Experion analysis (BioRad). Illumina HiSeq 2000 Experimental Factor: chronic myeloid leukemia disease Experimental Factor: accelerated phase chronic myeloid leukemia disease staging