Discover - Cerebellum

Genome wide methylome and whole proteome profiling was performed on cerebellum samples collected from Ptch1⁺/⁻ mice following neonatal γ irradiation (0 Gy, 0.1 Gy, 2 Gy). Genomic DNA was extracted from frozen cerebellar tissue and analyzed by reduced representation bisulfite sequencing (RRBS). Reads were aligned to the reference genome using Bismark, and methylation levels at CpG sites were quantified. Differential methylation analysis was performed using the methylKit R package. The average methylation at each chromosome and at each annotated transcript are determined on a per-sample basis. For the region-based analysis, the genome is tiled into 1 kilobase regions and significantly differentially methylated tiles are identified (methylation difference > 20%). Proteins were extracted from frozen cerebellar tissue, digested, and analyzed by DIA-PASEF mass spectrometry. Data were processed using Spectronaut against the SwissProt mouse database. Differential protein expressions were defined based on q-value 0.05, at least two unique peptides, and fold change ≥1.5 or ≤0.6.