biostudies-arrayexpressJan-Inge BjuneMus musculusfeaturecounts, Deseq2Hisat2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14723ME3 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 etcbiostudies-arrayexpressSequencing - 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 TapeStationSample 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Read counts were normalised with featurecounts and Deseq2 was run to get the expression matrixSequence Alignment - Hisat2 sequencing alignment tool was used for the alignment of the readsMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusJan-Inge BjunefalseRNA-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-792ME3 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 etc2025-05-17T00:00:00Z2024-12-23T17:43:21.17Z2024-12-23T17:43:21.17ZE-MTAB-14723ERP167401E-MTAB-13524E-MTAB-13525E-MTAB-13520E-MTAB-8200E-MTAB-8209E-MTAB-13540EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969