Project description:This analysis aimed to assess the effect of arborvitae (Thuja plicata) essential oil (AEO) in an in vitro model of cell lines derived from cervical cancer, namely HeLa and SiHa, by examining its influence on gene expression modulation. The working cell lines were HeLa, and SiHa. Total RNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model. Methodology: The execution of the bioinformatics pipeline analysis was carried out as follow: R (ver. 4.3.1), RStudio (ver. 2023.09.1 +494) and Galaxy (https://www.usegalaxy.orgaccessed on 02 February 2024) open-source platforms were used to analyze the Illumina raw data. The Quality Check was conducted through the FastQC tool (v0.74+galaxy0). Afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v44). The obtained output was the BAM files, of which the number of reads was counted by the FeatureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by the DESeq2 package for R (ver. 1.42. 0). The differential gene expression measurements were normalized by DESeq2's median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All genes with an adjusted p-value (p-adj) minus or equal to 0.05 and fold change (Log2FC) up to 2 or less than minus 2 were selected as differentially expressed genes (DEGs). Conclusions: Our study found that AEO regulates genes related with cell cycle regulation, cell growth, differentiation, and cell death in both cell lines, mainly through downregulation; however, its effect appears to be mediated by different pathways in each cell line.
