Project description:The aim of the project was the analysis of the bulk proteome and phosphoproteome in 3D organoids (tubuloids) from the adult mouse kidney. Proteome (nearly 9000 proteins) and phosphoproteome (nearly 16000 phospho sites) were compared in three biological (independent) replicates of epithelial organoids (early passage and long-term, 3-month cultures) and freshly isolated, MAC-sorted, Epcam-positive kidney epithelial cells. After collection of the organoids, Matrigel was removed using a non-enzymatic solution.
Project description:In this project hiPSC-derived β-like cells were studied in two different 3D enviromnets; size-adjusted cell aggregates (using Aggrewell™ plates) and inside alginate capsules. The hiPSC derived from a patient with maturity-onset diabetes of the young 1 (MODY1), which is a monogenic diabetes form, caused by a mutation in the HNF4A gene. We also generated and included a CRISPR/cas9 corrected isogenic control line. Human islets were also included as positive control. In the data analysis we compared to proteome of the cells in 3D environments compared to the frat 2D enviromnet. We found HNF4A mutation specific effects with both distinct 3D environments, where the cells are challenged differentially in term of oxygen, nutrient supply and cell-to-cell contact. We identified HNF4A mutation-specific phenotypes, including a unique proteome signature suggesting metabolic changes in the alginate bead environment, and mutation-specific cellular phenotypes and a unique proteome signature in the aggregation environment.
Project description:Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control- with 4-OHT-treated. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRβ), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of 4-OHT-induced degeneration of photoreceptor cells in the 3D-retinas. 4-OHT-induced gene expression in the 3D-retinas was measured at DD 26 when the photoreceptor cells were degenerated. Two-condition experiment, vehicle control- vs. 5 µM 4-OHT-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1 replicate.
Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that do not pattern 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains two samples - WT-pool, Mt-pool.
Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that failed to initiate 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains four samples - GdGFP, VxmCherry, WT-pool, Mt-pool.
Project description:Herein we compare mouse (C57B6/J background, 16 week old) adherent bone marrow stromal cell gene expression after 4 weeks of adipogenic differentiation in 3D versus 2D culture. Adipogenic differentiation was compared on a 3D silk scaffold versus a 2D (tissue culture plastic) surface using an microarray mRNA analysis.