GSM8691983: K27M_612137, experimental replicate 4; Mus musculus; Bisulfite-Seq
Tumor-bearing mouse brains were cut in half sagitally and then formalin fixed and parrafin embedded (FFPE).  Tumor areas were identified on H+E slides cut from the surface of each FFPE block.  Tumor was then microdissected from the corresponding areas of two unstained ten-micron sections from the FFPE block.  Genomic DNA was extracted from the microdissected tumor tissue via standard methods. The genomic DNA, spiked with lambda DNA, was fragmented into 200–400 bp pieces and bisulfite-treated to generate single-stranded DNA (ssDNA). During this process, unmethylated cytosines were converted to uracil, while methylated cytosines remained unchanged. Methylation sequencing adapters were ligated, and double-stranded DNA was synthesized. After size selection and PCR amplification, the library was prepared.