Briefly, the tissue samples were thawed, mounted and refrozen in OCT embedding media, then cryosectioned (6 μm thick sections) using a Tissue-Tek II cryostat.
Briefly, cerebellum and attached hindbrain were extracted from newborn (P0) CD1 mouse pups (Charles River Laboratories) and cut into 300 μm sagittal sections using a McIlwain tissue chopper.
24 Genomic DNA was extracted from 9 × 3.5‐μm FFPE sections using a QIAamp tissue kit in accordance with manufacturer's guidelines (Qiagen).
DNA was extracted from frozen sections containing ≥70% tumour cells and venous blood samples as described previously (12) and from FFPE tissue sections using a QIAamp DNA FFPE Tissue Kit (Qiagen).
Genomic DNA was extracted from these sections using a DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).
Total RNA was extracted from 5-μm whole FFPE tissue sections using a silica bead based, fully automated isolation method (VERSANT Tissue Preparation Reagents Kit; Siemens Healthcare Diagnostics, Tarrytown, NY, USA) [ 19- 21].
DNA was extracted from two 10 μm sections using an all-tissue DNA-extraction kit according to the manufacturer's protocol (GEN-IAL, Troisdorf, Germany).
After discarding the top few sections (to eliminate oxidised/contaminated tissue), viable tumour and adjacent stromal tissue areas were carefully macrodissected from tissue sections using a scalpel and dissecting microscope.
Briefly, 5 μm sections using a cryostat from frozen tissues were placed on poly- L-lysine-coated slides or silane-coated slides, and fixed in cold acetone for 10 min.
Tumour tissue samples were obtained from 5-μm-thick tissue sections using a LMD6000 laser microdissection system (Leica Microsystems, Wetzlar, Germany).
