Data for: RNA-seq data analysis of stimulated hepatocellular carcinoma cells treated with epigallocatechin gallate and fisetin reveals target genes and action mechanisms (Part2 - fisetin treatment)

In this study, we endeavor to compare gene expression alterations mediated by flavonoids epigallocatechin gallate (EGCG) and fisetin (FIS) through a comprehensive transcriptome analysis based on RNA-seq in human hepatocellular carcinoma HEP3B cells, upon perturbation with a mixture of prototypical stimuli mimicking conditions of tumor microenvironment (STIM), or under constitutive state (MEM). HEP3B cells, seeded the day before in a 6-well plate, were serum-starved for 4h and then treated with EGCG (100μM), FIS (10μM) or DMSO (0.1 % v/v) for 2h. Cells were subsequently exposed to a mixture of stimuli consisting of recombinant interleukins IL-6 (0.1μg/ml), IL-1B (0.01μg/ml) and tumor growth factor A (TGFA) (0.2μg/ml) and were further incubated for 22h. Samples of all possible treatment combinations of HEP3B cells i.e. EGCG, FIS, or DMSO at either MEM or STIM state were subjected to RNA extraction from two independent experiments.Total RNA was isolated using the PureLink RNA Mini Kit (Invitrogen, USA) according to the manufacturer’s instructions. Quantification and quality control of isolated RNA was performed by measuring absorbance at 260nm and 280nm on a NANODROP ONEC spectrophotometer (Thermo Scientific, USA). The RNA-seq run was performed on a NextSeq 500 Illumina platform that provided single-end reads of 85bp length. Quality assessment, library preparation (TruSeqLT) and the actual sequencing run was conducted in the Biomedical Research Foundation of the Academy of Athens (BRFAA) sequencing facility.
Herein, we provide (compressed in .bz2 file format) raw sequencing FASTQ files regarding the FIS treatment, along with a descriptive metadata file (FIS_metadata.pdf). Due to storage limitations, respective data about EGCG treatment are provided in a separate dataset entitled "Data for: RNA-seq data analysis of stimulated hepatocellular carcinoma cells treated with epigallocatechin gallate and fisetin reveals target genes and action mechanisms (Part1 - epigallocatechin gallate treatment)".

本研究旨在通过基于RNA测序的全面转录组分析，对比黄酮类化合物儿茶素没食子酸酯（EGCG）和芹菜素（FIS）介导的基因表达改变。该分析在人类肝细胞癌细胞HEP3B细胞中完成，细胞在经模拟肿瘤微环境条件（STIM）的典型刺激混合物扰动或构成状态（MEM）下进行处理。HEP3B细胞于前一天在6孔板中接种，饥饿培养4小时后，分别用EGCG（100μM）、FIS（10μM）或DMSO（0.1 % v/v）处理2小时。随后，细胞被暴露于由重组白细胞介素IL-6（0.1μg/ml）、IL-1B（0.01μg/ml）和肿瘤生长因子A（TGFA）（0.2μg/ml）组成的刺激混合物中，并进一步培养22小时。所有可能的HEP3B细胞处理组合样本，即EGCG、FIS或DMSO在MEM或STIM状态下的样本，均来自两个独立的实验，进行了RNA提取。RNA使用PureLink RNA Mini Kit（Invitrogen，美国）按照制造商的说明进行纯化。通过在NANODROP ONEC分光光度计（Thermo Scientific，美国）上测量260nm和280nm处的吸光度，对提取的RNA进行定量和质量控制。RNA测序在Illumina NextSeq 500平台上进行，提供了85bp长度的单端读数。质量评估、文库制备（TruSeqLT）和实际的测序运行在雅典科学院生物医学研究基金会（BRFAA）测序设施中进行。在此，我们提供了关于FIS处理的原始测序FASTQ文件（压缩为.bz2文件格式），以及一个描述性元数据文件（FIS_metadata.pdf）。由于存储限制，EGCG处理的相关数据提供在另一个名为“数据集：儿茶素没食子酸酯和芹菜素处理的刺激肝细胞癌细胞RNA测序数据分析揭示靶基因和作用机制（第1部分 - 儿茶素没食子酸酯处理）”的数据集中。