{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Michal Dudek"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17163"],"description":["In vitro studies have been invaluable in unravelling the complexity of the core clock mechanism and their responses to various stimuli. However, fidelity of in vitro cell culture as a proxy for studying tissue and cell type specific rhythmic processes in vivo has not been rigorously tested. This study compared the rhythmic transcriptomes between chondrocytes synchronised in vitro with three methods and in vivo cartilage rhythmic transcriptome. Using high-throughput RNA-sequencing of primary chondrocytes synchronized via heat shock, dexamethasone, and osmotic stress, we demonstrate that while all three methods robustly induce circadian rhythms in the expression of the core clock genes, each method results in distinct rhythmic transcriptome with little overlap."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Primary articular chondrocytes were isolated from five-day-old mice and cultured in DMEM/F12 supplemented with 10% FBS, Pen-Strep. To synchronise circadian rhythms, chondrocytes at 90% confluence in 35 mm cell culture dishes were incubated with 100 nM of dexamethasone for 60 min. Afterwards, media was changed and dishes were sealed with 40 mm glass cover slips. Sealed dishes were placed in an incubator at 37 °C for 112 hours. At 112 hours half the dishes (heat shock condition) were moved to an incubator at 43 °C for 60 min. The other dishes (dexamethasone condition) remained in an incubator at 37 °C and 100 nM dexamethasone were added to the culture media approximately 15 min prior to the end of the heat pulse. All dishes were then returned to the incubator at 37 °C and","Nucleic Acid Extraction - Total RNA was isolated using the PureLink RNA Mini Kit (Thermo Fisher) as per manufacturer’s instructions.","Library Construction - 50ng of mRNA per sample was used for library generation. Libraries were generated using the TruSeq Stranded mRNA assay (Illumina) according to the manufacturer’s protocol.","Sequencing - Libraries were sequenced (2 × 200 bp paired-end reads) in the HiSeq 4000 instrument (Illumina). The output data was demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software v2.20.0.422."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Quality control and pre-processing of FASTQ files was performed using FastQC v 0.11.3 and MultiQC v1.8. Sequence adapters were removed and reads were quality trimmed using Trimmomatic v0.39","Data Transformation - Reads were then mapped to the Ensembl GRCm38/mm10 mouse genome and counts per gene were calculated using STAR v2.7.3a with annotation from GENCODE M25. Raw reads are deposited as processed data."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000","Standard cell culture","PureLink RNA Mini Kit (Thermo Fisher)","TruSeq Stranded mRNA assay (Illumina)"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Michal Dudek"],"additional_accession":[]},"is_claimable":false,"name":"Circadian time series of mouse primary chondrocytes exposed to heat shock or dexamethasone","description":"In vitro studies have been invaluable in unravelling the complexity of the core clock mechanism and their responses to various stimuli. However, fidelity of in vitro cell culture as a proxy for studying tissue and cell type specific rhythmic processes in vivo has not been rigorously tested. This study compared the rhythmic transcriptomes between chondrocytes synchronised in vitro with three methods and in vivo cartilage rhythmic transcriptome. Using high-throughput RNA-sequencing of primary chondrocytes synchronized via heat shock, dexamethasone, and osmotic stress, we demonstrate that while all three methods robustly induce circadian rhythms in the expression of the core clock genes, each method results in distinct rhythmic transcriptome with little overlap.","dates":{"release":"2026-07-20T00:00:00Z","modification":"2026-07-20T17:48:17.493Z","creation":"2026-06-15T13:02:37.725Z"},"accession":"E-MTAB-17163","cross_references":{"ENA":["ERP195065"],"Biostudies":["E-MTAB-11040","E-MTAB-3428"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}