biostudies-arrayexpressJan KubovčiakHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15569To better understand how mechanical signals influence liver cancer cell behavior, we employed transcriptomic analysis using bulk RNA sequencing. Alexander, HepG2, and Huh7 cells were cultured for 48 hours on ESS dishes with varying stiffness to assess their global transcriptional responses to different extracellular matrix (ECM) conditions. Differential expression analysis revealed extensive transcriptional changes in all three cell lines, with Huh7 cells exhibiting the strongest response - demonstrated by the highest number of significantly altered genes and pathways.biostudies-arrayexpressSample Collection - Cells were harvested from ESS dishes during RNA extraction protocol.Library Construction - Libraries were prepared using Lexogen Quantseq kit according to the manufacturer's protocol.Nucleic Acid Extraction - Total RNA was extracted using RNeasy® Mini Kit according to the manufacturer's protocol.Sequencing - Libraries were sequenced on the Illumina NextSeq® 500 instrument using 75 bp single-end configuration on high-output flowcell.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Sequencing reads were processed using the bioinformatic pipeline nf-core/rnaseq v3.10.1. Individual steps included removing sequencing adaptors and low-quality reads with Trim Galore and cutadapt, mapping to reference genome GRCh38 (Ensembl annotation version 104) with STAR and quantifying expression on gene level with salmon.Data Transformation - Sequencing reads were mapped with STAR and expression on gene level was quantified from mapping reads with salmon. Estimated gene-level counts are provided as processed files.UnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAHomo sapiensJan KubovčiakOleg LunovfalseRNA sequencing of Alexander, HepG2, and Huh7 cells cultured on ESS dishes with different stiffnesses (1.5, 15, 28 kPa and reference GPa) for 48 hTo better understand how mechanical signals influence liver cancer cell behavior, we employed transcriptomic analysis using bulk RNA sequencing. Alexander, HepG2, and Huh7 cells were cultured for 48 hours on ESS dishes with varying stiffness to assess their global transcriptional responses to different extracellular matrix (ECM) conditions. Differential expression analysis revealed extensive transcriptional changes in all three cell lines, with Huh7 cells exhibiting the strongest response - demonstrated by the highest number of significantly altered genes and pathways.2026-05-11T00:00:00Z2026-05-13T14:11:35.257Z2025-09-12T10:26:04.541ZE-MTAB-15569ERP179973EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184