SRX4681233 GSM3389725 SRP161783 SRS3774774 GSM3389725 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389725 GSM3389725 GEO Accession GSM3389725 SRX4681234 GSM3389726 SRP161783 SRS3774775 GSM3389726 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389726 GSM3389726 GEO Accession GSM3389726 SRX4681235 GSM3389727 SRP161783 SRS3774776 GSM3389727 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389727 GSM3389727 GEO Accession GSM3389727 SRX4681236 GSM3389728 SRP161783 SRS3774810 GSM3389728 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389728 GSM3389728 GEO Accession GSM3389728 SRX4681237 GSM3389729 SRP161783 SRS3774777 GSM3389729 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389729 GSM3389729 GEO Accession GSM3389729 SRX4681238 GSM3389730 SRP161783 SRS3774778 GSM3389730 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389730 GSM3389730 GEO Accession GSM3389730 SRX4681239 GSM3389731 SRP161783 SRS3774779 GSM3389731 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389731 GSM3389731 GEO Accession GSM3389731 SRX4681240 GSM3389732 SRP161783 SRS3774780 GSM3389732 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389732 GSM3389732 GEO Accession GSM3389732 SRX4681241 GSM3389733 SRP161783 SRS3774781 GSM3389733 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389733 GSM3389733 GEO Accession GSM3389733 SRX4681242 GSM3389734 SRP161783 SRS3774782 GSM3389734 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389734 GSM3389734 GEO Accession GSM3389734 SRX4681243 GSM3389735 SRP161783 SRS3774783 GSM3389735 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389735 GSM3389735 GEO Accession GSM3389735 SRX4681244 GSM3389736 SRP161783 SRS3774784 GSM3389736 Bisulfite-Seq GENOMIC RANDOM genomic DNA extracted and purified using the Zymo Duet Kit DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina). Bisulfite-Seq 150 bp paired end on Illumina HiSeqX HiSeq X Ten gds 303389736 GSM3389736 GEO Accession GSM3389736