{"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-16022"],"description":["The purpose of this experiment was to generate an RNAseq dataset of human cardiomyocytes with lower levels of FOXO3 exposed to doxorubicin for 24 hours. Stable knock-down of FOXO3 was achieved using lentiviral shRNA construct. As negative control cells bearing an shRNA targeting GFP was used"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Poly(A) libraries were generated using the Zephyr G3® NGS automated system with the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198–02, PerkinElmer). Library preparation included NEXTFLEX® Poly(A) Beads 2.0 (NOVA-512992, PerkinElmer) for mRNA enrichment and NEXTFLEX® Unique Dual Index Barcodes (NOVA-512923, PerkinElmer) for sample multiplexing. Each library was prepared using 100 ng of total RNA as input, with RNA integrity numbers (RIN ≥ 8). A total of 13 PCR cycles were performed during library amplification.","Sequencing - Sequencing was carried out on the Illumina NovaSeq 6000 using an S2 flow cell, generating paired-end reads with 100 cycles per read.","Sample Collection - After the exposure, cells were washed once with PBS and subsequently lysed in 0.5 mL QIAzol Lysis Reagent (79306, Qiagen).","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"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Twan van den Beucken"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of of doxorubicin exposed SV40 immortalized human cardiomyocytes with FOXO3 knock-down or shGFP control","description":"The purpose of this experiment was to generate an RNAseq dataset of human cardiomyocytes with lower levels of FOXO3 exposed to doxorubicin for 24 hours. Stable knock-down of FOXO3 was achieved using lentiviral shRNA construct. As negative control cells bearing an shRNA targeting GFP was used","dates":{"release":"2025-12-29T00:00:00Z","modification":"2026-05-27T16:04:21.572Z","creation":"2025-11-13T14:29:04.81Z"},"accession":"E-MTAB-16022","cross_references":{"ENA":["ERP183898"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}