Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (6mA)

This dataset encompasses comprehensive analyses of the epigenetic mark N6-methyladenine (6mA) in human cell lines, focusing on its role under hypoxic conditions and its association with cancer progression. Addressing the challenge of 6mA's low abundance in mammals, we have innovated the 6mA-ChIP-exo-5.1 method. This technique enhances the sensitivity and accuracy of 6mA detection, employing exonuclease-dependent antibody-based approaches combined with whole genome amplification (WGA) to minimize potential noise and false positives. FaDu, a head and neck cancer cell line, was purchased from Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The mycoplasma absence was tested by Mycoplasma PCR Detection Kit (abm) before the experiments. Knockdown of METTL4 was achieved using a previously established method with lenti-virus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2, and 94% N2 at 37°C for 18 hours.

本数据集涵盖人类细胞系中表观遗传标记N6-甲基腺嘌呤（N6-methyladenine，6mA）的系统性分析，重点探究其在低氧条件下的生物学功能及与癌症进展的关联。针对哺乳动物中6mA丰度极低这一研究难点，本团队研发了6mA-ChIP-exo-5.1检测方法。该技术依托依赖核酸外切酶的抗体富集策略，并结合全基因组扩增（whole genome amplification，WGA），有效提升了6mA检测的灵敏度与准确性，最大限度降低了潜在噪声与假阳性结果。头颈部癌细胞系FaDu购自生物资源保存及研究中心（Bioresource Collection and Research Center，BCRC，中国台湾新竹）。该细胞系培养于添加10%胎牛血清（Fetal Bovine Serum，FBS）、1 mM丙酮酸钠及1×抗生素-抗真菌混合液（Gibco）的德式改良伊格尔培养基（Dulbecco’s modified Eagle’s medium，DMEM）中，培养条件为37℃、5% CO₂。实验开始前，采用支原体PCR检测试剂盒（Mycoplasma PCR Detection Kit，abm）对细胞进行了支原体污染阴性验证。通过前期已建立的慢病毒感染方法，成功实现了METTL4基因的敲低。低氧处理时，将细胞置于37℃、含1% O₂、5% CO₂及94% N₂的培养环境中孵育18小时。