characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-07-13T15:37:59Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-07-13T15:37:59Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112319209
characteristics.characteristic: External Id
characteristics.text: Kennedy Institute of Rheumatology, University of Oxford
characteristics.characteristic: INSDC center name
characteristics.text: 2023-07-13T15:37:59Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-07-13T15:37:59Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14424721
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12498:visceral-adipocyte-341
characteristics.characteristic: Submitter Id
characteristics.text: 14 to 15
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: large adipocyte
characteristics.characteristic: cell_type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Mice (3 male + 3 female per experimental group) were treated with water or 2% DSS for 5 days and then maintained at water for 2 more days until mice were sacrificed at day 7. Visceral adipose tissues (epididymal, retroperitoneal and omental) from each mouse were pooled. Adipose tissues were collected and digested in DMEM containing 1% fatty acid-free BSA (Sigma, 126609), 5% HEPES (Gibco, 15630-056), 0.2mg/mL Liberase TL (Roche, 5401020001) and 20µg/mL DNaseI (Roche, 11284932001). Tissues were minced in digestion medium and incubated for 25-30min at 37°C at 180rpm. Tissues were further broken down by pipetting using wide-bore tips and filtered through a 100µm mesh. Digestion was quenched by adding medium containing 2mM EDTA. Adipocyte and stromal vascular fraction were separated by centrifugation (700g, 10min). Floating adipocyte fraction was removed and collected in a fresh tube. After 5min rest, subnatant (under floating adipocyte layer) was aspired and remaining adipocytes taken up in 1mL TRI reagent (T9424, Sigma). Total RNA was extracted using TRI reagent (T9424, Sigma) and chloroform following RNeasy Mini Kit (74104, Qiagen) manufacturer instructions. RNA was eluded in RNase-free water and stored at -80°C until further processing. Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 7.3 and 9.5. Input material was normalised to 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified (14 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104).
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: intestinal disease
characteristics.characteristic: disease
characteristics.text: Atg7 knockout
characteristics.characteristic: genotype
characteristics.text: 341
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: adipose tissue
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: C57BL/6J
characteristics.characteristic: strain
characteristics.text: visceral-adipocyte-341
characteristics.characteristic: title