ATAC-seq analysis for intravesical BCG in bladder cancer

BCG vaccination can boost innate immune responses via trained immunity (TI), resulting in an increased resistance to respiratory viral infections. Assay for transposase accessible chromatin (ATAC), including tagmentation, library preparation and sequencing were performed by Genewiz (Azenta Life Sciences, MA, USA) on PBMCs from two BCG-treated NMIBC patients at baseline and during BCG (mid) as well as from three healthy donors. This dataset include the pipeline for preprocessing of raw data including mapping to the hg38 reference genome using bowtie2 and peak calling by MACS2. Differentially accessible regions in proximity to annotated genes between the two time points (during BCG versus baseline) were identified using the R packages csaw and edgeR and resulting data files are provided.卡介苗（BCG）接种可通过训练性免疫（trained immunity, TI）增强先天免疫应答，进而提升机体对呼吸道病毒感染的抵抗能力。转座酶可及性染色质检测（Assay for transposase accessible chromatin, ATAC）涵盖转座酶标签化、文库构建与测序环节，相关实验由美国马萨诸塞州的Genewiz（Azenta生命科学公司）完成。实验样本包含2名接受卡介苗治疗的非肌层浸润性膀胱癌（non-muscle invasive bladder cancer, NMIBC）患者的外周血单个核细胞（peripheral blood mononuclear cells, PBMC），采样时点分别为基线期与卡介苗治疗中期；同时纳入3名健康供者的外周血单个核细胞样本。本数据集包含原始测序数据的预处理流程，具体包括使用bowtie2将测序reads比对至hg38参考基因组，以及通过MACS2进行染色质开放峰识别。研究人员通过R软件包csaw与edgeR，鉴定了两个采样时点（卡介苗治疗中期 vs 基线期）的注释基因邻近区域内的差异染色质可及性区域，相关结果数据文件已随本数据集提供。