{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan-Inge Bjune"],"organism":["Mus musculus"],"software":["featurecounts, Deseq2","Hisat2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14723"],"description":["ME3 control and Irx3-KO mouse beige-like preadipocytes were grown in proliferation medium until confluence (day -2), before induction of adipogenesis on day 0 followed by adipogenic differentiation for 9 days. Cells were treated with either DMSO or 0.5 uM ML-792 for 24h either from day -2 to day -1 or day 0 to day 1, or throughout the differentiation from day 0 to 9 (n =3 replicate wells for each condition) before collection by trypsination, centrifugation and snap-freezing in liquid N2 on days -1, 1 and 9, respectively. Cell pellets were kept at -80C until RNA isolation.  RNA was isolated using the RNeasy protocol with on-column DNase treatment.  *** insert info about RNA QC, library prep flow cell, bioinformatics etc"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - NovaSeq 6000; NovaSeq S2 flowcell using standard workflow method; 2x100bp paired-end reads.","Sample Treatment - Cells were treated with either DMSO or 0.5 uM ML-792 for 24h either from day -2 to day -1 or day 0 to day 1, or throughout the differentiation from day 0 to 9 (n =3 replicate wells for each condition) before collection by trypsination, centrifugation and snap-freezing in liquid N2 on days -1, 1 and 9, respectively. Cell pellets were kept at -80C until RNA isolation.","Nucleic Acid Extraction - RNA was isolated using phenol/guanidine-based lysis followed by chloroform extraction and silica-based spin column purification of the aquous phase according to instructions of the RNeasy Lipid Tissue kit (Qiagen). RNA quantity and integrity was assessed by Qubit fluorometric quantification.","Library Construction - Library prep: Illumina Stranded mRNA, Ligation kit  Quantification of libraries: Illumina MiSeq Nano sequencing Library QC on Agilent TapeStation","Sample Collection - On day of harvest, cells were collection by trypsination, centrifugation and snap-freezing in liquid N2 on days -1, 1 and 9, respectively. Cell pellets were kept at -80C until RNA isolation.","Growth Protocol - ME3 control and Irx3-KO mouse beige-like preadipocytes were grown in proliferation medium (Amniomax -C100, 1% PEST, 7.5% FBS, 7.5% C100 and 1% L-glut) in 6-well plates pre-coated with 0.1% gelatine until confluence (day -2), before induction of adipogenesis on day 0 followed by adipogenic differentiation for 9 days.   Cells were treated with Induction medium (861 nM Insulin, 1 uM Dexamethasone, 0.5 mM IBMX and 1 uM Rosiglitazone added to the prolif medium) from day 0-2, followed by differentiation medium (only 861 nM Insulin added to the prolif medium) from day 2-4 and proliferation medium from day 4-9."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Read counts were normalised with featurecounts and Deseq2 was run to get the expression matrix","Sequence Alignment - Hisat2 sequencing alignment tool was used for the alignment of the reads"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Jan-Inge Bjune"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of mouse ME3 control and Irx3-KO cells on days -1, 1 and 9 of adipogenic differentiation after treatment with DMSO or the SUMOylation inhibitor ML-792","description":"ME3 control and Irx3-KO mouse beige-like preadipocytes were grown in proliferation medium until confluence (day -2), before induction of adipogenesis on day 0 followed by adipogenic differentiation for 9 days. Cells were treated with either DMSO or 0.5 uM ML-792 for 24h either from day -2 to day -1 or day 0 to day 1, or throughout the differentiation from day 0 to 9 (n =3 replicate wells for each condition) before collection by trypsination, centrifugation and snap-freezing in liquid N2 on days -1, 1 and 9, respectively. Cell pellets were kept at -80C until RNA isolation.  RNA was isolated using the RNeasy protocol with on-column DNase treatment.  *** insert info about RNA QC, library prep flow cell, bioinformatics etc","dates":{"release":"2025-05-17T00:00:00Z","modification":"2024-12-23T17:43:21.17Z","creation":"2024-12-23T17:43:21.17Z"},"accession":"E-MTAB-14723","cross_references":{"ENA":["ERP167401"],"Biostudies":["E-MTAB-13524","E-MTAB-13525","E-MTAB-13520","E-MTAB-8200","E-MTAB-8209","E-MTAB-13540"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}