Similar Datasets
Project description:H9 human embryonic stem cells and Isthmic organizer (IsO) like cells
| PRJNA413986 | ENA
Project description:Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. The genomic expression values of each sample are then measured with oligonucleotide arrays. From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation. A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes. Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes. Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function. We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms. These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation. Keywords: development, organizer, noggin, dkk-1, xenopus, gastrulation
2006-06-30 | GSE3368 | GEO
Project description:Gene expression profiling reveals a potential role of Iso towards hepatic differentiation of hAESCs. hAESCs were isolated from discarded term placenta and were treated with 20 μM Iso for 10 days. Microarray gene expression profiling was conducted for biological replicates of Iso-treated hAESCs on day 10 and untreated control cells on day 0, and day 10.
2020-06-25 | GSE153149 | GEO
Project description:The objective of this study was to induce the production of isthmic organizer (IsO)-like cells capable of secreting fibroblast growth factor (FGF) 8 and WNT1 from human embryonic stem cells (ESCs). The precise modulation of canonical Wnt signaling was achieved in the presence of the small molecule CHIR99021 (0.6 μM) during the neural induction of human ESCs, resulting in the differentiation of these cells into IsO-like cells having a midbrain-hindbrain border (MHB) fate in a manner that recapitulated their developmental course in vivo. Resultant cells showed upregulated expression levels of FGF8 and WNT1. The addition of exogenous FGF8 further increased WNT1 expression by 2.6 fold. Gene ontology following microarray analysis confirmed that IsO-like cells enriched the expression of MHB-related genes by 40 fold compared to control cells. Lysates and conditioned media of IsO-like cells contained functional FGF8 and WNT1 proteins that could induce MHB-related genes in differentiating ESCs. The method for generating functional IsO-like cells described in this study could be used to study human central nervous system development and congenital malformations of the midbrain and hindbrain.
| S-EPMC5824020 | biostudies-literature
Project description:Identify gene expression patterns of different neural precursor cells derived from human embryonic stem cells.
2015-04-30 | GSE67383 | GEO
Project description:Identify gene expression patterns of different neural precursor cells derived from human embryonic stem cells. The total of 12 samples were analyzed which could be grouped into 4 groups
2015-04-30 | E-GEOD-67383 | biostudies-arrayexpress
Project description:LPS plus ISO and LPS plus PGE2 had non-additive effects on gene expression in RAW 264.7 cells Keywords: time course
2006-06-06 | GSE4964 | GEO
Project description:Gene expression profiling reveals a potential role of Iso towards hepatic differentiation of hAECs.
2020-04-17 | GSE148777 | GEO
Project description:The generation of cardiomyocytes from human embryonic stem cells (hESC) enables a variety of potential therapeutic and diagnostic applications. However, progress is challenged by the low efficiency of cardiomyocyte differentiation. Recently, Kattman et al., 2011 showed that individual hESC lines required proper balance of the Activin A and BMP4 signaling for efficient cardiac differentiation, presenting their differentiation protocols for several human and mouse ESC lines. However, two of the most utilized hESC lines, H7 and H9, were not included. Therefore, we set out to verify the published methodology for highly efficient cardiac specification and investigate the cardiac differentiation in the H7 and H9 ESC lines. Our studies examined a range of time points for the initial culture of hESC as embryoid bodies (EB) prior to transfer to monolayer culture, as well as, concentrations of Activin A and BMP4 in the medium formulations. The results highlight an efficient protocol for reproducibly generating cultures with approximately 50% cardiomyocytes from H7 and H9 ESC lines.
| S-EPMC3908295 | biostudies-literature
Project description:The hop plant, Humulus lupulus L., contains an exceptionally high content of secondary metabolites, the hop iso-α-acids, which possess a range of beneficial properties including antiseptic action. Studies performed on the mode of action of hop iso-α-acids have hitherto been restricted to lactic acid bacteria. The present study investigates molecular mechanisms of hop iso-α-acid resistance in the model eukaryote Saccharomyces cerevisiae. Growth inhibition occurred at concentrations of hop iso-α-acids that were an order of magnitude higher than those found with hop-tolerant prokaryotes. Chemostat-based transcriptome analysis and phenotype screening of the S. cerevisiae haploid gene deletion collection were used as complementary methods to screen for genes involved in hop iso-α-acids detoxification and tolerance. Further analysis of deletion mutants confirmed that yeast tolerance to hop iso-α-acids involves two major processes: active export of iso-α-acids across the plasma membrane and active proton pumping into the vacuole by the V-ATPase to enable vacuolar sequestration of iso-α-acids. Furthermore, iso-α-acids were shown to affect cellular metal homeostasis by acting as strong zinc and iron chelator.
2009-11-13 | GSE15094 | GEO