title: W56-33
organism: Mus musculus
description: Protocols: ME3 cells were differentiated for 0, 1 and 7 days, trypsinated, pelleted, snap-frozen in liquid nitrogen and stored at -80C. 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. The cells were thawed on ice, and treated with DNase to remove DNA released from dead cells before lysis in ice-cold ATAC seq lysis buffer from the ATAC-Seq Kit (Active Motif, Carlsbad, CA, USA) for 2 min. Crude nuclei extracts were spun down at 600xg for 10 min at 4C and nuclei were resuspended in 40 µL 1X Tagmentation buffer. The integrity of the nuclei was verified under microscope, counted, and 50,000 nuclei was transferred pr sample for tagmentation. Tagmentation and indexing was performed according to the instructions of the ATAC-seq Kit (Catalog No. 53150, Active Motif). Briefly, nuclei were incubated in tagmentation buffer for 30 min at 37C with gentle mixing every 5 min. Tagmented DNA was purified by a standard silica spin column method provided by the kit. Indexing/PCR amplification of the library performed using unique combinations of i5 and i7 indexing primers. Indexed DNA was cleaned up using SPRI magnetic beads. Library QC was performed by a D5000 ScreenTape assay
attributes.tag: ENA first public
attributes.value: 2025-05-12
attributes.tag: External Id
attributes.value: SAMEA114578488
attributes.tag: INSDC center name
attributes.value: University of Bergen
attributes.tag: INSDC last update
attributes.value: 2023-11-03T20:13:46Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13525:W56-33
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: ME3 beige-like preadipocytes
attributes.tag: cell_type
attributes.value: small adipocyte
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: day 7 of adipogenic differentiation
attributes.tag: genetic modification
attributes.value: Irx3-KO
attributes.tag: genotype
attributes.value: Rb−/−
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: adipose tissue
attributes.tag: sample name
attributes.value: E-MTAB-13525:W56-33
attributes.tag: scientific_name
attributes.value: Mus musculus