Chromatin accessibility in B16 and 4T1 cell lines with decitabine treatment [ATAC-seq]

The goal of ATAC-seq is to identify the open chromatin regions in the B16 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for ATAC-seq libraries. We mapped about 30-100 million reads per sample to M.musculus (mm10) with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed M.Musculus have dispartate chromatin accessibility after Decitabine treatment Nuclei from B16 and 4T1 cells were extacted and transposed, and cDNA libraries were generated for deep sequencing, in triplicate, using HiSeq 4000 or NovaSeq S4

本研究中转座酶可及性测序（ATAC-seq）的实验目标为鉴定经地西他滨（Decitabine）处理后的B16细胞与4T1细胞中的开放染色质区域。每组设置3次生物学重复，总计制备了12组ATAC-seq文库。采用Bowtie2流程将每个样本的约3000万至1亿条测序读段（reads）比对至小家鼠（M.musculus）参考基因组mm10版本。通过ChIPseeker工具鉴定开放染色质区域，并筛选校正后P值小于0.05的区域。研究结果显示，经地西他滨处理后，小家鼠细胞的染色质可及性存在显著差异。提取B16与4T1细胞的细胞核并进行转座反应，随后生成cDNA文库用于深度测序，所有实验均设置3次生物学重复，测序平台采用HiSeq 4000或NovaSeq S4。