Cervical Cancer derived cell lines: Gene Expression Profile
This analysis aimed to identify differentially expressed genes in Cervical Cancer derived cell lines. The working cell lines were SiHA, HeLa, C33A, and HaCaT as control. mRNA 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 according to the following description: Rstudio (v2023.06.1+524) and Galaxy open-source platforms were used to analyze the Illumina raw data. The Quality Check was conducted through the FastQC tool (v0.12.1). 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 v43). 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 tool (v2.11.40.8). 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 chemokine genes with an adjusted p-value (adj p) 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). Some genes from the resulting outputs were validated through qPCR.Conclusions: Our study found 5850 differentially expressed genes for SiHa cell lines, 6698 for HeLa, and for C33a, 6707 DEGs.