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BBN处理的小鼠开展RNA测序（RNA-seq）分析，采用nf-core社区开发的rnaseq流程（版本1.2），该流程是一套基于Nextflow的经精心整理验证的生物信息学流程集合。简要而言，测序数据的质量通过FastQC（版本0.11.8）进行评估。使用TrimGalore（版本0.5.0）完成测序接头的切除，同时采用默认参数的Cutadapt（版本1.18）进行低质量序列的修剪。经修剪的测序读段（reads）通过STAR（版本2.6）比对至小家鼠（M. musculus）的mm10（GRC38）参考基因组。基因表达量通过Salmon（版本1.2.0）进行定量。基因ID的前缀对应不同处理组别：C代表对照组，B代表BBN处理组，E代表厄洛替尼处理组，T代表曲美替尼处理组。