{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan-Inge Bjune"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13520"],"description":["A map of open chromatin in WT beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation.  100.000 cells were collected in duplicates at each timepoint by trypsination. Cells were  slowly frozen at -80C in culture media containing 5% DMSO before shipping on dry ice to Active Motif for open chromatin profiling.  In brief, chromatin was isolated from the cells followed by Tn5 transposase-mediated insertion of sequencing primers into open chromatin regions. After library preparation, high-throughput sequencing (Illumina) was performed and reads were then aligned to the mm10 genome using Bowtie2 (Version 2.3.4.3).."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Performed by in-house protocols by Active Motif, based on published methods:  Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10(12): 1213–8.","Sample Collection - ME3 beige-like preadipocytes were grown to confluency and induced for adipogenic differentiation 2 days post confluency (day 0) by addition of adipogenic cocktail. On days 0, 1 and 7 of differentiation, cells were trypsinized, counted and 100,000 cells were slowly frozen down at -80C in culture medium containing 5% DMSO.  Frozen cells were shipped on dry ice to Active Motif for processing.","Nucleic Acid Extraction - In-house protocols by Active Motif, based on published methods:  Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10(12): 1213–8.","Growth Protocol - Cells were grown in AmnioMAX-C100medium supplementedwith 7.5% FBS, 7.5% C100 (all from Thermo Fisher Scientific,Waltham, MA, USA), 1% penicillin-streptomycin (PEST) (Sigma, St.Louis, MO, USA) and 2 mM L-glutamine (Sigma) at 37 °C and 5% CO2.Adipogenic differentiation was initiated three days post confluency(day 0) by induction medium containing 5 μg/mL Insulin (INS)(Sigma), 1 μMDexamethasone (DEX) (Sigma), 0.5mMisobutylmethylxanthine(IBMX) (Sigma) and 1 μM Rosiglitazone (ROSI) (CaymanChemical, Ann Arbor, MI, USA). From day 2 to day 4 only insulin wasadded to the basal medium and from day 4 to 7 cells were grown inthe basal medium.","Library Construction - Performed by in-house protocols by Active Motif, based on published methods:  Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10(12): 1213–8."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were first filtered for mapping quality ≥ 30 (samtools Version 1.7-2) and duplicated reads, as well as reads mapping to the mitochondria, were subsequently removed (picardTools Version 2.8.1.1). Peak calling was performed via Macs2 (Version 2.1.1). Peak sets were first filtered using blacklisted regions from the ENCODE project [91], then converted into a simple annotation format for submission to the Rsubread featureCounts (Version 1.6.0) package. Using this consensus peak set as an annotation guide, each unmerged bam file was submitted to featureCounts and the subsequent count matrix was input into RStudio for peak annotation and visualization."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Active Motif Catalog No. 53150","Illumina HiSeq 3000"],"study_type":["ChIP-seq"],"species":["Mus musculus"],"pubmed_authors":["Jan-Inge Bjune"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq of WT mouse beige ME3 cells on days 0, 1, and 7 of adipogenic differentiation","description":"A map of open chromatin in WT beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation.  100.000 cells were collected in duplicates at each timepoint by trypsination. Cells were  slowly frozen at -80C in culture media containing 5% DMSO before shipping on dry ice to Active Motif for open chromatin profiling.  In brief, chromatin was isolated from the cells followed by Tn5 transposase-mediated insertion of sequencing primers into open chromatin regions. After library preparation, high-throughput sequencing (Illumina) was performed and reads were then aligned to the mm10 genome using Bowtie2 (Version 2.3.4.3)..","dates":{"release":"2025-05-16T00:00:00Z","modification":"2024-11-26T12:02:31.491Z","creation":"2023-11-03T21:29:37.929Z"},"accession":"E-MTAB-13520","cross_references":{"ENA":["ERP153191"],"Biostudies":["E-MTAB-13524","E-MTAB-13525"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0003816","EFO_0004184"]}}