biostudies-arrayexpressJunqing ZhangRattus norvegicushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15094This study employs bulk RNA-seq to investigate the transcriptomic changes in rat epicardial mesothelial cells (EMCs) under different oxygen conditions. We compare gene expression profiles between normoxia (20% O2, 48 hours), hypoxia (0.1% O2, 48 hours), and reoxygenation (recovery after 24 hours hypoxia). The goal is to identify key pathways and differentially expressed genes involved in the cellular response to oxygen deprivation and recovery. This work provides insights into the molecular mechanisms of ischemia-reperfusion injury and may contribute to understanding cardiac adaptation to hypoxia.biostudies-arrayexpressLibrary Construction - RNA samples were sent to Novogene (UK) for library construction, quality control and sequencing.Sequencing - RNA samples were sent to Novogene (UK) for library construction, quality control and sequencing.Nucleic Acid Extraction - Total RNA was extracted from stressed EMCs using QIAzol Lysis Reagent (Qiagen) followed by purification with the Reasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a Nanodrop 2000 spectrophotometer (Thermo Scientific), with samples exhibiting A260/A280 ratios between 1.8 and 2.1 and A260/A230 ratios > 2.0 considered suitable for downstream analysis. RNA integrity was further verified using an Agilent 5400 Fragment Analyzer, with RNA integrity numbers (RIN) > 8.0 required for library preparation.Sample Collection - Cell lines from the culture were collected after epicardial conditioned media collection.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw data (raw reads) in fastq format was processed to remove reads containing adapter, reads containing ploy-N and low-quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome (genome ID: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4) using Hisat2. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNARattus norvegicusJunqing ZhangPilar Ruiz-LozanofalseTranscriptomic profiling of rat epicardial cells under normoxic, hypoxic and reoxygenation conditionsThis study employs bulk RNA-seq to investigate the transcriptomic changes in rat epicardial mesothelial cells (EMCs) under different oxygen conditions. We compare gene expression profiles between normoxia (20% O2, 48 hours), hypoxia (0.1% O2, 48 hours), and reoxygenation (recovery after 24 hours hypoxia). The goal is to identify key pathways and differentially expressed genes involved in the cellular response to oxygen deprivation and recovery. This work provides insights into the molecular mechanisms of ischemia-reperfusion injury and may contribute to understanding cardiac adaptation to hypoxia.2025-10-03T00:00:00Z2025-10-03T01:02:46.838Z2025-04-25T11:04:15.854ZE-MTAB-15094ERP171974EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184