GSM4970319: AK149; Homo sapiens; Bisulfite-Seq
Enrichment libraries of GBM-targeted regulatory DNA segments were constructed using the SureSelect Methyl-Seq protocol #G9651A using one microgram genomic DNA per reaction. Quality and size distribution of the bisulfite-converted captured  segments were verified by TapeStation nucleic acids system (Agilent) assessments. Target enrichment efficiency and coverage was evaluated via sequencing of  the bisulfite-converted libraries. Variable regulatory regions were defined as the regions carrying H3K4me1 marks in all tumors, and also H3K27ac in at least 25% of the tumors, but not in at least other 25% of the tumors. RNA probes were designed to target all methylation sites within these regions, utilizing the SureDesign tool (https://earray.chem.agilent.com/suredesign/). Probe duplication was applied in cases (n=8,652) of >5 CpG sites within the 120 bp span of the probes. Repetitive regions were identified by BLAT and excluded from the design. Custom-designed biotinylated RNA probes were ordered from Agilent Technologies (https://www.agilent.com).