SRX2492781 GSM2458790 SRP096751 PRJNA361295 SRS1922352 SAMN06229963 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458790 GSM2458790 GEO Accession GSM2458790 SRX2492782 GSM2458791 SRP096751 PRJNA361295 SRS1922353 SAMN06229962 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458791 GSM2458791 GEO Accession GSM2458791 SRX2492783 GSM2458792 SRP096751 PRJNA361295 SRS1922354 SAMN06229964 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458792 GSM2458792 GEO Accession GSM2458792 SRX2492784 GSM2458793 SRP096751 PRJNA361295 SRS1922355 SAMN06229961 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458793 GSM2458793 GEO Accession GSM2458793 SRX2492785 GSM2458794 SRP096751 PRJNA361295 SRS1922356 SAMN06229960 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458794 GSM2458794 GEO Accession GSM2458794 SRX2492786 GSM2458795 SRP096751 PRJNA361295 SRS1922357 SAMN06229968 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458795 GSM2458795 GEO Accession GSM2458795 SRX2492787 GSM2458796 SRP096751 PRJNA361295 SRS1922358 SAMN06229967 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458796 GSM2458796 GEO Accession GSM2458796 SRX2492788 GSM2458797 SRP096751 PRJNA361295 SRS1922359 SAMN06229966 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458797 GSM2458797 GEO Accession GSM2458797 SRX2492789 GSM2458798 SRP096751 PRJNA361295 SRS1922360 SAMN06229965 OTHER GENOMIC other DNA isolation: The pellet was lysed in the solution containing 2% sodium dodecyl sulphate and 25 mM EDTA. Proteins were precipitated by adding 1/3 volume of 10 M ammonium acetate and removed as a pellet by centrifugation. DNA was precipitated from the supernatant with isopropanol, washed with 70% ethanol and dissolved in TE (10 mM TRIS pH 8.0, 1 mM EDTA). Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels were digested with 20 units of SmaI endonuclease (NEB) for 8 hours at 25°C. Subsequently, 20 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA with methylation-specific signatures at the ends of restriction fragments was end repaired using dCTP, dGTP and dATP (0.4 mM final concentration of each) and 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB). Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA). Illumina HiSeq 2500 gds 302458798 GSM2458798 GEO Accession GSM2458798