characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-11-09T00:26:45Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-11-09T00:26:45Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112183539
characteristics.characteristic: External Id
characteristics.text: OXFORD
characteristics.characteristic: INSDC center name
characteristics.text: 2023-11-09T00:26:45Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-11-09T00:26:45Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14293431
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12414:Sample 17
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: 10% control conditioned media for 20h Organoids were cultured as previously described.1 Colonic crypts were isolated from longitudinal opened and cleaned colon tissue of Atg16l1fl/fl mice by 2mM EDTA in PBS incubation for 90min at 4°C. The tissue was vigorously resuspended in PBS/10% FCS and the supernatant containing the crypts filtered through a 100μm cell strainer and pelleted. Crypts were seeded in 20μl Matrigel/well (Corning) in a 24-well plate. After polymerisation of the Matrigel, 400ul of complete organoid medium was added [Advanced Dulbecco's Modified Eagle Medium (DMEM)/F12 supplemented with 1% Pen/Strep, 10mM HEPES, 1X GlutaMax, 50ng/ml mEGF, 1× N2, 1× B27 (all from Invitrogen), 1mM N-acetylcysteine (NAC), 10μM RhoK-inhibitor (Y-27632 dihydrochloride monohydrate) (both from Sigma) and conditioned medium containing Wnt3a (20%), Noggin (20%) or R-spondin (10%)]. The conditioned media were generated from Rspol-Fc Hek 293T cells (kind gift from Dr. Calvin Kuo, Stanford) and Nog-Fc Hek 293T cells (kind gift from Dr. Gjis van den Brink, Amsterdam) and Wnt3A L cells (ATCC CRL-2647). The medium was changed every 2-3d and organoids were expanded over several passages before they were used for experiments with indicated stimuli. Ref: 1 Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009). Qiagen Rneasy Kit Illumina Truseq mRNA kit
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: Atg16l1fl/fl
characteristics.characteristic: genotype
characteristics.text: intestinal organoid
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: crypt of Lieberkuhn of colon
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: Sample 17
characteristics.characteristic: title