characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-04-19T00:19:02Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-04-19T00:19:02Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112344843
characteristics.characteristic: External Id
characteristics.text: 1) Department of Morphology, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Belgium 2) Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), Leuven, Belgium
characteristics.characteristic: INSDC center name
characteristics.text: 2023-04-19T00:19:02Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-04-19T00:19:02Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14455753
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12544:scrEXT341
characteristics.characteristic: Submitter Id
characteristics.text: 7
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: mixed incisor organoid derived cell and dental pulp cell
characteristics.characteristic: cell_type
characteristics.text: IncisorAssembloid_Control
characteristics.characteristic: cohort
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Tooth assembloids (2 replicates per condition) were dissociated into single cells using 0.25% Trypsin (Gibco; supplemented with 5M ROCKi) treatment and mechanical trituration and collected in 0.04% BSA (in PBS) using a Flowmi 40 um cell strainer (Sigma-Aldrich). Tooth assembloids were established using a modified protocol as described previously (Hemeryck et al., 2022). Briefly, after dissociating P2-3 organoids and molar DPSCs into single cells, both cell types were combined in round-bottom low-attachment plates (96-well; Greiner). Using a layered approach, first 5,000 DPSCs were seeded by sedimentation (300 g for 1 min at 4 °C), followed by 5,000 molar tooth organoid- or incisor tooth organoid-derived cells (300 g for 1 min at 4 °C) (Nakao et al., 2007). The cells were provided with 10% growth-factor reduced Matrigel and 90% of either a 1:1 mixture of tooth organoid medium (TOM) + pulp medium (PM) or differentiation medium (DM) + pulp differentiation medium (PDM) (see ‘treatment protocol’ for medium compositions). After 24 h incubation at 37 °C and 5% CO2, the formed structures were collected and plated in 20 L droplets of Matrigel (70%) to generate tooth assembloids. Assembloids were maintained in the 1:1 media mixtures at 37 °C and 5% CO2. Assembloids were maintained for 6 days in 1:1 media mixtures of TOM/PM or DM/PDM before collection. TOM consisted of serum-free defined medium (SFDM; DMEM/F12 1:1, 5 mg/l human transferrin, 5mg/l insulin Hybrimax from bovine pancreas, 35mg/L penicillin, 50mg/L streptomycin, 600uL/L ethanol, 50µl/L catalase, 1g/L NaHCO3, 0.5% BSA) supplemented with 0.5 uM A83-01, 1X B27, 100 ng/mL cholera toxin, 20 ng/mL bFGF, 200 ng/mL FGF8, 100 ng/mL FGF10, 2 mM L-glutamine, 100 ng/mL IGF1, 1X N2, 1.25 mM N-acetyl L-cysteine, 10 mM Nicotinamide, 100 ng/mL noggin, 200 ng/mL RSPO1, 10 uM SB202190, 100 ng/mL SHH, 200 ng/mL WNT3A and 20 ng/mL EGF. PM consisted of α-MEM supplemented with 10% FBS, 103 units/mL ESGRO recombinant LIF protein, 2.5 ng/mL bFGF and 1% penicillin-streptomycin. DM consisted of SFDM supplemented with 1X B27, 100 ng/mL BMP2, 50 ng/mL BMP4, 20 ng/mL EGF, 20 ng/mL bFGF and 4 ng/mL TGF-beta1. PDM consisted of PM supplemented with 100 uM ascorbic acid, 5 mM beta-glycerophosphate and 10 uM dexamethasone. Single cell suspensions were converted to barcoded Drop-seq libraries by using the Chromium Single Cell 3’ V2 Library, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics; Pleasanton, California, USA), aiming for an estimated 5,000 cells per library. Single cell libraries were prepared with the Chromium Single Cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit from 10X Genomics.
characteristics.characteristic: description
characteristics.text: juvenile stage
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: mixed tooth organoid medium and pulp medium
characteristics.characteristic: growth condition
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: incisor tooth
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: scrEXT341
characteristics.characteristic: title