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)
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 EGCG treatment, along with a descriptive metadata file (EGCG_metadata.pdf). Due to storage limitations, respective data about FIS 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 (Part2 - fisetin treatment)".