{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Yinuo Ma"],"instrument_platform":["NA","Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16488"],"description":["This study aimed to investigate the transcriptional effects of asperuloside (ASP) on inflammatory chondrocytes and its potential mechanisms in osteoarthritis (OA). ATDC5 cells were stimulated with TNF-α and IL-1β to mimic the inflammatory environment of OA, followed by treatment with either asperuloside (ASP) or PBS as a vehicle control. An untreated group served as a baseline control. Total RNA was extracted and subjected to RNA-seq to identify differentially expressed genes and pathways involved in inflammation, extracellular matrix metabolism, and cartilage homeostasis. The results provide transcriptomic insights into the anti-inflammatory and chondroprotective effects of asperuloside."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA-seq libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, USA) following the manufacturer’s protocol.  After adapter ligation and PCR amplification, libraries were quantified and validated using a Qubit fluorometer and Agilent Bioanalyzer.","Nucleic Acid Extraction - Total RNA was extracted from ATDC5 cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.  RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was confirmed with an Agilent 2100 Bioanalyzer (RIN ≥ 8.0).","Sample Collection - ATDC5 cells were cultured under standard conditions (37°C, 5% CO₂) in DMEM/F12 medium supplemented with 5% FBS and antibiotics.  Cells were divided into three groups: untreated control, TNF-α/IL-1β–stimulated group (OA model), and TNF-α/IL-1β–stimulated group treated with asperuloside (ASP).  After 24 hours of treatment, cells were harvested for RNA extraction.","Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads (PE150).  Raw reads were subjected to quality control, including adapter trimming and low-quality base removal, before downstream analysis."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Yinuo Ma"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of ATDC5 chondrocytes treated with asperuloside under TNF-α and IL-1β stimulation compared with PBS-treated and untreated controls","description":"This study aimed to investigate the transcriptional effects of asperuloside (ASP) on inflammatory chondrocytes and its potential mechanisms in osteoarthritis (OA). ATDC5 cells were stimulated with TNF-α and IL-1β to mimic the inflammatory environment of OA, followed by treatment with either asperuloside (ASP) or PBS as a vehicle control. An untreated group served as a baseline control. Total RNA was extracted and subjected to RNA-seq to identify differentially expressed genes and pathways involved in inflammation, extracellular matrix metabolism, and cartilage homeostasis. The results provide transcriptomic insights into the anti-inflammatory and chondroprotective effects of asperuloside.","dates":{"release":"2026-07-01T00:00:00Z","modification":"2026-07-01T01:04:19.702Z","creation":"2026-01-02T14:52:38.201Z"},"accession":"E-MTAB-16488","cross_references":{"ENA":["ERP187206"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0004184"]}}