Prado et al_bulk RNA seq mouse experiments

RNA-seq analysis of BBN treated mice was performed using the rnaseq pipeline (ver. 1.2) from the nf-core community, a nextflow collection of curated bioinformatic pipelines. Briefly, sequencing quality was assessed using FastQC (ver. 0.11.8). TrimGalore (v.0.5.0) was used for adapter removal, and Cutadapt (ver. 1.18) with default parameters was used for low-quality trimming. Trimmed reads were mapped to the M. musculus genome mm10 (GRC38) using STAR (ver. 2.6). Genes were quantified using Salmon (ver. 1.2.0). gene_id prefixes correspond to treatment groups: C = control, B = BBN, E = erlotinib, T = trametinib.本研究针对经N-丁基-N-(4-羟丁基)亚硝胺（BBN）处理的小鼠开展RNA测序（RNA-seq）分析，所用流程为nf-core社区开发的rnaseq流程（版本1.2）——nf-core社区是一个基于Nextflow框架、汇集经人工审核整理的生物信息学流程的社区。简言之，本研究使用FastQC（版本0.11.8）评估测序数据质量；采用TrimGalore（版本0.5.0）切除接头序列，同时使用默认参数的Cutadapt（版本1.18）完成低质量序列修剪。随后使用STAR（版本2.6）将经修剪的reads比对至小鼠（Mus musculus）基因组mm10（GRC38版本），并通过Salmon（版本1.2.0）进行基因表达量定量。基因ID的前缀对应不同处理分组：C为对照组，B为BBN处理组，E为厄洛替尼（erlotinib）处理组，T为曲美替尼（trametinib）处理组。