Genome-wide profiling of Tbx6myc binding during zebrafish somitogenesis
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE57332 | GEO | 2014/11/15
SECONDARY ACCESSION(S): PRJNA246287
REPOSITORIES: GEO
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Project description:Identification of Tbx6 genomic binding sites during zebrafish somitogenesis in order to identify Tbx6 targets genes Duplicate anti-myc ChIP samples with associated input for heat shocked Tg(hsp70l:tbx6Myc)v8 embryos, plus single paired anti-myc ChIP and input in wild type embryos - 3x ChIP samples; 3x input samples
2014-11-15 | E-GEOD-57332 | biostudies-arrayexpress
Project description:We established two iPSC-derived 3D models recapitulating human somitogenesis, Somitoids and Segmentoids. Somitoids recapitulate the temporal sequence of somitogenesis, with all cells undergoing differentiation and morphogenesis in a synchronous manner. On the other hand, Segmentoids recapitulate the spatio-temporal features of somitogenesis, including gene expression dynamics, tissue elongation, sequential somite morphogenesis, and polarity patterning. They therefore provide an excellent proxy to study human somitogenesis.
2022-02-02 | GSE195467 | GEO
Project description:Cell-type specific regulation of a small number of growth factor signal transduction pathways generates diverse developmental outcomes. The zinc finger protein Churchill (ChCh) is a key effector of fibroblast growth factor (FGF) signaling during gastrulation. ChCh is largely thought to act by inducing expression of the multifunctional Sip1 (Smad Interacting Protein 1). We investigated the function of ChCh and Sip1a during zebrafish somitogenesis. Knockdown of ChCh or Sip1a results in misshapen somites that are short and narrow. As in wild-type embryos, cycling gene expression occurs in the developing somites in ChCh and Sip1a compromised embryos, but expression of her1 and her7 is maintained in formed somites. In addition, tail bud fgf8 expression is expanded anteriorly in these embryos. Finally, we found that blocking FGF8 restores somite morphology in ChCh and Sip1a compromised embryos. These results demonstrate a novel role for ChCh and Sip1a in repression of FGF activity.
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Project description:This SuperSeries is composed of the following subset Series:; GSE7012: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of C2C12 myoblast line; GSE7015: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model Experiment Overall Design: Refer to individual Series
2008-06-15 | E-GEOD-7054 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
2011-11-17 | E-GEOD-32900 | biostudies-arrayexpress
Project description:Scoliosis is a common disorder, affecting one out of every twenty females. Some forms of scoliosis are congenital, resulting from disruptions in early spinal development. The spinal column is patterned during a cycling process called somitogenesis, and is the first musculoskeletal structure formed during development. Genes in the notch signaling pathway regulate somitogenesis, and display oscillatory expression in synchrony with somite formation. During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. The periodicity and components of the human clock have recently been described by our group (William et al., Dev Biol, 2007). In that publication, we showed that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression, including known cycling genes such as HES1 that displayed a period of 5 hours. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Studies in mouse cell lines, including fibroblasts and PC12 neuronal cells, by R. Kageyema (Kyoto University, Hirata et al., Science, 2002) have shown that a number of mouse cell types can be synchronized to display oscillatory expression. In this study, we extend our analysis of human cells to human primary fibroblasts. Developing an in vitro model of somitogenesis using human mesenchymal stem cells and fibroblasts; a. Induce cycling gene expression in human mesenchymal stem cells (MSC) and fibroblasts and identify oscillatory genes (using Affymetrix U133 GeneChips®). Compare lists of oscillatory genes identified in these two human cell types. b. Characterize and validate mouse homologues of oscillatory genes for expression during somitogenesis. Using notch and wnt pathway mutants and cultured half embryos, determine if these oscillatory genes also display cycling expression during somitogenesis. We hypothesized that human fibroblasts could be synchronized to display oscillatory expression of notch and wnt pathway genes, including the marker gene HES1. Preliminary quantitative analysis by Taqman-based Real-Time PCR for these samples confirms that HES1 expression displays oscillatory expression. Homo sapiens fibroblasts were maintained in culture medium (DMEM high glucose with 10% fetal bovine serum, FBS), which was replaced twice weekly. The cells were then seeded at a density of 6,000-10,000 cells/cm2 and expanded in DMEM high glucose with 10% FBS. After 5-7 days of incubation at 37C in a humidified atmosphere containing 5% carbon dioxide, cells were detached with 0.05% trypsin for 2 minutes at confluency. Cells were synchronized using low serum treatment, which has been described previously for Hes1 (Hirata et al., 2002). Cell culture synchronization is required to assay oscillatory expression levels, otherwise the oscillations of individual cells would be out of phase and cancel one another. Synchronized cells will gradually desynchronize, leading to diminished oscillatory amplitude. Briefly, synchronization was carried out as follows: T-25 cm flasks were set up in parallel. These cells were grown to 90% confluence in DMEM supplemented with 10% FBS (UCB-MSC), then incubated in DMEM with only 0.2% FBS for 24 hours, and returned to DMEM supplemented with FBS. Samples were collected at 1 hr. intervals from 0 to 12 hours. In addition, an unsynchronized cell culture was sampled. Total RNA was isolated from cells in culture using the RNeasy Mini Kit (Qiagen) and quantitated using a Nanodrop 2000. Experiment Overall Design: A biological replicate of the submitted project (hCycle11) time-series was carried out in parallel has been collected (hCycle12). We have evaluated both biological replicates by Q-PCR. We have selected hCycle11 for HG-U133A Plus 2.0 analysis, and we reserve hCycle12 for possible future microarray analysis or comparison by Q-PCR.
2008-10-21 | E-GEOD-11854 | biostudies-arrayexpress
Project description:The oscillations of the somitogenesis clock are linked to the fundamental process of vertebrate embryo segmentation, yet little is known about their generation. In zebrafish, it has been proposed that Her proteins repress the transcription of their own mRNA. However, in its simplest form, this model is incompatible with the fact that morpholino knockdown of Her proteins can impair expression of their mRNA. Simple self-repression models also do not account for the spatiotemporal pattern of gene expression, with waves of gene expression shrinking as they propagate. Here we study computationally the networks generated by the wealth of dimerization possibilities amongst transcriptional repressors in the zebrafish somitogenesis clock. These networks can reproduce knockdown phenotypes, and strongly suggest the existence of a Her1-Her7 heterodimer, so far untested experimentally. The networks are the first reported to reproduce the spatiotemporal pattern of the zebrafish somitogenesis clock; they shed new light on the role of Her13.2, the only known link between the somitogenesis clock and positional information in the paraxial mesoderm. The networks can also account for perturbations of the clock by manipulation of FGF signaling. Achieving an understanding of the interplay between clock oscillations and positional information is a crucial first step in the investigation of the segmentation mechanism.
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Project description:During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes. This SuperSeries is composed of the SubSeries listed below.
2018-04-27 | GSE106587 | GEO
Project description:We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA-seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development.
2021-03-30 | GSE143208 | GEO
Project description:Reconstruction of human Somitogenesis with pluripotent stem cells
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