Project description:scRNAseq of primary fetal liver (6 post conceptional weeks), fetal biliary organoids, hepatoblast organoids, hepatoblast organoids after withdrawl of Wnt and transfer to hepatozyme medium, hepatoblast organoids after TGFb treatment.
Project description:This experiment aims to define DGE when hiPSC derived brain organoids are exposed for long (chronic) or short (pulse) time to T3. Additionally, a comparison regarding T3 responsive genes can be assessed for two different brain organoids systems: cerebral organoids (CO) and Neural Stem Cell derived Organoids (NSCO). CO correspond to unguided differentiation following Lancaster et al. 2013. NSCO are neurospheres derived as desribed in https://dx.doi.org/10.17504/protocols.io.3byl4j6kzlo5/v1
Project description:Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, especially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of the experiment was to evaluate the effects of treatment of pitavastatin (PIT), prochloperazine (PCZ) and combination (PIT + PCZ) on LU-NB-2 PDX derived organoid model. In our experiments we observed synergistic effects on cell viability and cell death of those two compounds and further RNA-seq was intended to decipher effects of the combination on the neuroblastoma cells. Experimental Workflow: Sample Preparation: Tumor organoids were generated from PDX models of high-risk neuroblastoma patients with MYCN amplification. Treatment: LU-NB-2 PDX organoids were dissociated to single cells aseeded in T25 flasks, allowed to grow for 24 h, and treated for 48 h with the combination of PCZ +PIT (1.6 µM and 6.7 µM, n = 8), PCZ only (1.6 µM, n = 8), PIT only (6.7 µM, n = 8), or DMSO (n = 8). The treatment resulted in a ~15% decrease in NB cell viability in the combination group. RNA Extraction: Total RNA was extracted from the treated and control organoids. Library Preparation and Sequencing: RNA-seq libraries were prepared and sequenced to generate high-throughput sequencing data. Data Analysis: Differential gene expression analysis was performed to compare the treated samples against the untreated controls, aiming to elucidate the molecular effects of each treatment.
Project description:Human neural organoid models have become an important tool for studying neurobiology. In this work, we compared Matrigel to an N-cadherin peptide-functionalized gelatin methacryloyl hydrogel (termed GelMA-Cad) for culturing cortical neural organoids. Specifically, we compare five materials: (1) Matrigel, (2) GelMA-Cad with high crosslinker (HC), (3) GelMA-Cad with low crosslinker (LC), (4) GelMA HC and (5) GelMA LC. We profiled these organoids at the earliest stages to understand potential differences in radial glia formation.
Project description:Organoids were established from patients with ovarian cancer. DNA was extracted from organoids and primary tissue to investigate whether organoids retain the same genomic abnormalities and disease-associated features.
Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of 12 cerebral organoids.
Project description:Organoids were established from patients with ovarian cancer. DNA was extracted from organoids and primary tissue to investigate whether organoids retain the same genomic abnormalities and disease-associated features.
Project description:Human neural organoid models have become an important tool for studying neurobiology. In this work, we compared Matrigel to an N-cadherin peptide-functionalized gelatin methacryloyl hydrogel (termed GelMA-Cad) for culturing cortical neural organoids. Specifically, we compare five materials: (1) Matrigel, (2) GelMA-Cad with high crosslinker (HC), (3) GelMA-Cad with low crosslinker (LC), (4) GelMA HC and (5) GelMA LC. We determined that both mechanical properties and peptide presentation can tune cell fate and diversity in gelatin-based matrices during differentiation. Of particular note, cortical organoids cultured in GelMA-Cad produce higher numbers of neurogenic and ciliated radial glia and upper-layer excitatory neurons—an important population for modeling neurodegenerative disease—compared to GelMA and Matrigel controls.
Project description:Knowledge on tooth epithelial stem cells and corresponding biology in humans is sparse. Here, we developed an organoid model, typically replicating epithelial tissue stem cell biology, starting from human tooth. Dental follicle (DF), isolated from extracted wisdom teeth, efficiently generated long-term expandable epithelial organoids. The organoids displayed a tooth stemness phenotype as present in DF’s Epithelial Cell Rests of Malassez, a compartment deemed to contain tooth epithelial stem cells. To further decode the organoids in more granular detail, we applied scRNA-seq analysis on DF-derived organoids (passage 1 (P1) and P4) together with their primary tissue. Additionally, to decipher the amelogenesis-resembling process that takes place in the tooth organoids upon differentiation, we performed scRNA-seq analysis of P4 organoids switched to mineralization-inducing medium for 8 days.