{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Twan van den Beucken"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16038"],"description":["The purpose of this experiment was to generate an additional RNAseq dataset of human cardiomyocytes exposed to doxorubicin for 24 hours. For robustness 7 biological replicas were generated per exposure group."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - 50 ng of total RNA isolated from SV40 immortalized cardiomyocytes samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. We performed 18 PCR cycles were performed during library preparation. RNA-Seq libraries were quantified on a Qubit 2.0 Fluorometer (ThermoFisher) and quality control checked on the 2200 TapeStation System (Agilent).","Sample Collection - After the exposure, cells were washed once with PBS and subsequently lysed in 0.5 mL QIAzol Lysis Reagent (79306, Qiagen).","Sequencing - RNA-Seq libraries were sequenced on an S4 Illumina flowcell 35 cycles (v1.5) (Illumina) on a NovaSeq 6000 Sequencing System (Illumina) in single-end mode.","Nucleic Acid Extraction - Total RNA was extracted using chloroform and isopropanol precipitation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing reads were quality-checked and aligned to the reference genome using STAR. Gene-level count matrices were generated and imported into DESeq2 for normalization. Size-factor normalization was performed using the median-of-ratios method to correct for library size and compositional differences."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Anthracyclines such as doxorubicin (DOX) are widely used and effective chemotherapeutic agents, but their clinical use is limited by dose-dependent cardiotoxicity, known as anthracycline-induced cardiotoxicity (AIC). Previously, we identified FOXO3 as a key transcription factor involved in cardiomyocyte stress response pathways. However, its precise role in modulating DOX sensitivity remains incompletely understood. This study aims to investigate the role of FOXO3 in cardiomyocyte transcriptional regulation and its impact on DOX-induced stress responses. By analyzing transcriptomic alterations in FOXO3-deficient cells, we seek to deepen the knowledge on FOXO3 and its potential role in cardioprotection. We generated a novel RNA sequencing dataset from immortalized human cardiomyocytes (hCMs) treated with DOX to compare global gene expression changes between FOXO3-depleted and control cells. Functional pathway analysis was conducted to identify dysregulated biological processes. FOXO3 nuclear translocation following DOX exposure was assessed through immunofluorescence, and key transcriptional changes were validated using RT-qPCR. We observed that DOX treatment induces FOXO3 nuclear translocation in hCMs and that FOXO3 depletion alters the transcriptional landscape of cardiomyocytes under basal conditions as well as after DOX exposure. Deregulated expression of genes related to DNA repair, oxidative stress response and apoptotic signaling, may explain the increased DOX sensitivity of FOXO3 depleted hCMs."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["FOXO3 mediated gene expression modulates doxorubicin sensitivity in human cardiomyocytes"],"pubmed_authors":["J.G. Faber ,  M. van Herwijnen ,  D. Hauser ,  S. Daemen ,  F. Caiment ,  T. van den Beucken","Twan van den Beucken"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of doxorubicin exposed SV40 immortalized human cardiomyocytes","description":"The purpose of this experiment was to generate an additional RNAseq dataset of human cardiomyocytes exposed to doxorubicin for 24 hours. For robustness 7 biological replicas were generated per exposure group.","dates":{"release":"2025-12-14T00:00:00Z","modification":"2026-05-27T14:50:25.929Z","creation":"2025-11-06T10:39:05.718Z"},"accession":"E-MTAB-16038","cross_references":{"pubmed":["40854400"],"ENA":["ERP183757"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1016/j.tox.2025.154267"]}}