Project description:We performed Drop-seq using alveolar organoids cultured in MTECplus medium to identify cell types, gene expression patterns and signaling pathways in ex vivo condition.
Project description:A unique HTR2C+ alveolar macrophage (AM) population is enriched in the female lungs, which can metabolically reprogram bone marrow-derived macrophages (BMDMs). We collected the conditional culture medium from cultured HTR2C- or HTR2C+ AMs to incubate with BMDMs. Next, the BMDMs were harvested for RNA sequencing.
Project description:hiPSC from 2 different donors were differentiated into alveolar-like organoids (iPSC-aLOs) as previously described (DOI: 10.1038/s41596-019-0220-0). iPSC-aLOs were either kept in \"dome\" culture embedded in extracellular matrix or inverted in apical-out conformation to allow influenza H3N2 infection. Apical-out iPSC-aLOs were exposed or not to H3N2. At 24hs post-infection iPSC-aLOs were collected and dissociated into single cells. Samples were multiplexed using membrane lipid barcoding and we followed 10X Genomics instructions from single cell encapsulation to NGS. This data set is useful to compare iPSC-aLOs cell composition both in dome and apical-out culture conditions and iPSC-aLOs response to influenza virus H3N2 infection at a single timepoint of 24hs post-infection at MOI =1. Each sample (HUB 07-09) contains multiplexed conditions: control in dome culture, control in apical out (both non infected), infected 24 hpi. Due to human data sensitivity concerns, this experiment was submitted with processed data only.
Project description:To investigate extravillous trophoblast (EVT) differentiation mechanisms, we generated human trophoblast organoids (hTOr) from human trophoblast stem cells (hTSCs) and analyzed them by single-nucleus RNA sequencing. Organoids were initially cultured under simulated microgravity using a ClinoStar bioreactor for 11 days to establish proper trophoblast architecture, then embedded in Matrigel and cultured in EVT differentiation medium for 14 days. This study examines the cellular composition and differentiation trajectories during EVT specification, providing insights into human placental development and trophoblast lineage decisions. Two independent hTSC lines (CT27 and CT29) were used as biological replicates to ensure reproducibility and capture potential line-specific variations in EVT differentiation capacity.asts.
Project description:Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in injury-repair. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development through differentiation of lung progenitor organoids to AT2 cells and benchmarking against primary AT2 organoids.
Project description:Liver has abundant regenerative capacity, but hepatocytes cannot be cultured long-term in vitro. Activation of FXR signaling induced iHOs with both hepatocyte traits and proliferative potential. To investigate the transcriptomic analysis of iHOs, we performed bulk RNA-seq analysis of organoids in different passages and single cell RNA-seq analysis of iHOs. Compared to 2D-iPS-Heps and organoids in other culture conditions, iHOs have expression profiles more similar to primary human hepatocytes and human fetal liver cells. Single cell RNA-seq revealed iHOs have a fraction that co-expresses hepatocyte markers and proliferation markers.
Project description:Mouse thymic epithelial cell organoids, cultured in (1) expansion medium, (2) differentiation medium, or (3) differentiation medium with Rank ligand and retinoic acid (DM+RR), were FACS sorted into plates to follow the SORT-seq protocol (Muraro et al., 2016).
Project description:Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-seq (scRNA-seq) analysis of the HTII-280 positive and HTII-280+ /EpCAM+populations from total 6 donors from periferal tissue was performed, and analysis revealed subclusters enriched for stem cell signature genes. We found that these alveolar progenitors in organoid culture in vitro show phenotypic lineage plasticity as they can yield alveolar or bronchial cell type progeny. The direction of the differentiation is dependent on the presence of the GSK-3β inhibitor, CHIR99021. By RNA-seq analysis of GSK-3 βknockdown organoids, we identify additional functional candidate target genes and pathways which contribute to alveolar differentiation independent of Wnt signaling
Project description:Human induced pluripotent stem cells (hiPSCs) were differentiated into alveolar epithelial cells in the fibroblast-dependent (FD) or fibroblast-free (FF) alveolar organoids (AO). Then the epithelial cells in FD-AOs or FF-AOs were subjected to scRNA-seq. Then, human iPSC-derived AT1 (iAT1) cells were demonstrated to be included in FD-AOs, not in FF-AOs. In addition, XAV-939 increased iAT1 cell population in FD-AOs.