Project description:This experiment investigates transcriptomic differences between two SKOV3 ovarian cancer cell strains, S1 (CW1) and S2 (SM), to assess how clonal evolution and culture conditions influence gene expression. Bulk RNA sequencing (RNA-seq) was performed on cells cultured in both 2D monolayers and 3D spheroids. The study aims to identify differentially expressed genes and pathways associated with epithelial-mesenchymal transition (EMT), proliferation, and metabolic regulation. The sequencing data were processed using standard bioinformatics pipelines, including quality control, alignment, normalization, and differential expression analysis.
Project description:Substrate topography has emerged as a novel regulator of cell fate behaviour in keratinocytes (Zijl, Acta Biomater, 2019). Specifically, small circular micropillars (S1) can induce the differentiation of spread cells, and larger triangular substrates (S2) can inhibit differentiation in kerinocytes. Here we investigated the potential molecular mechanisms behind these processes. We chose timepoints previously shown to be associated with differentiation in suspension cultures (Mishra, eLife, 2017), in order to find early regulators of the differentiation process. Our results show a delay in differentiation on S2 substrates and an upregulation of differentiation pathways on S1. Beyond this, no clear mechanistic regulators of the differentiation program were found.
Project description:The series represent gene expression profiles of HMT3522 S1 mammary epithelial cells cultured as 2D monolayers or in 3D reconstituted basement membrane (rBM) and treated with the death ligand TRAIL. Keywords: Genetic modification; response to death induction
Project description:In order to better understand the biological roles of critical SARS-CoV-2 proteins, we determined and compared the host transcriptomic responses of the HL-CZ human promonocytic cell line upon transfection with key viral genes encoding the spike S1 subunit, S2 subunit, nucleocapsid (NP) protein, NSP15 (endoribonuclease), and NSP16 (2′-O-ribose-methyltransferase).
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001, a bacteria-derived polysaccharide. Gene microarrays were used to observe the global gene expression in SKOV3 cells cultured with adhesion condition (2D, control) or with low adhesion condition (FP001) and identified distinct classes of up or down-regulated genes. SKOV3 cells were cultured for 11 days in normal attachment plates with normal medium (as control) or low-attachment plates with FP001 containing medium. Each sample was collected three times.
Project description:To study the effect of rs1192691 on ovarian cancer cells, we generated SKOV3(CC) from SKOV3(A/A) using CRISPR/Cas9 technology and performed RNA-seq.