GSM8586061: Medulloblastoma frozen tumor, SHH, M007RB06; Homo sapiens; OTHER
DNA were extracted from frozen MB samples using the standard phenol-chloroform procedure. The quality and quantity of DNA were assessed using Nanodrop (Thermo Fisher Scientific) and Qubit (Thermo Fisher Scientific). Quantification of DNA was performed using the Qubit Fluorometer (Quant-iT dsDNA BR Assay Kit; Thermo Fisher Scientific) and quality assessment was carried out using TapeStation (Genomic DNA screenTape; Agilent) following the manufacturer's instructions. For whole-genome Nanopore sequencing, DNA libraries were prepared using the SQK-RBK004 rapid barcoding kit from Oxford Nanopore Technologies. Two types of flow cells were used: MinION R9.4.1 (FLO-MIN106D) and Flongle R9.4.1 (FLO-FLG001). For MinION flow cells, 400 ng of DNA were tagmented, barcoded, repaired, and pooled in batches of six samples before adaptor ligation. Sequencing involved multiplexing six libraries, with each batch taking 48 to 72 hours per MinION R9.4.1 flow cell. For Flongle flow cells, the same SQK-RBK004 kit (Oxford Nanopore Technologies) was used, but 200 ng of DNA per tumor sample was sequenced individually on a Flongle flow cell for 24 hours. All sequencing was performed on MinION Mk1B or Mk1C devices, and sequencing runs were initiated and monitored using MinKnow software from Oxford Nanopore Technologies.