Single-cell transcriptomic analysis of zebrafish fli1b mutants
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE290550 | GEO | 2025/03/26
REPOSITORIES: GEO
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Project description:The goal of this experiment was to identify using tissue specific transgenic zebrafish (Fli:EGFP), genes of interest important for embryonic vascular development. Keywords: time course, GFP cell isolation, zebrafish The experiment contained 6 samples. A18, A24 = total RNA isolated from 18 and 24 hpf zebrafish embryo; B2, C and D2=RNA isolated from GFP positive cells sorted at 18, 24 and 28 hpf respectively from Tg(Fli1:EGFP) embryos; E2 = RNA isolated from GFP positive cells sorted at 18 hpf from Tg(Flk:GRCFP) embryos.
2010-05-22 | E-GEOD-12516 | biostudies-arrayexpress
Project description:Junctional adhesion molecule 3 (Jam3) is a cell adhesion molecule that is involved in cell-cell interaction, cell migration, and cell polarization in many tissue including the epithelium, endothelium, and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells, the role of Jam3 in hematopoietic or vascular development is still unknown. In this study, a zebrafish jam3b mutant line, jam3b-sa37, was used for the cap analysis gene expression (CAGE) sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo.
2019-06-01 | GSE114416 | GEO
Project description:Human oncogenes involved in the development of hematological malignancies have been widely used to model experimental leukemia. Here, we used the fli1 promoter in zebrafish to target the expression of oncogenic HRAS to endothelial cells, including the hemogenic endothelium and observed the development of a myelo-erythroid proliferative disease. In larvae, the pathological phenotype is characterized by some disruption of the vascular system with prominent expansion of the caudal hematopoietic tissue, increase of expression of stem cell markers and myelo-erythroid specific genes and production of a large number of l-plastin leukocytes. In mosaic juveniles, increased number of hematopoietic blasts and arrest of myeloid maturation was found in kidney marrow. Peripheral blood showed delays of erythrocyte maturation and increased number of circulating myeloid progenitors. We found that the abnormal phenotype is associated with a down regulation of the Notch pathway as shown by the decrease of expression of Notch target genes, whereas overexpressing an activated form of Notch together with the oncogene prevents the expansion of the myelo-erythroid compartment. This study identifies the downregulation of the Notch pathway following an oncogenic event in the hemogenic endothelium as an important step in the pathogenesis of myelo-erythroid diseases and describes a number of potential effectors of this transformation. Methods: mRNA profiles of transgenic zebrafish overexpressing the oncogene HRAS in endothelial cells (Tg(fli1ep:GAL4FF)ubs3; Tg(UAS:eGFP-HRASV12)io006); or expressing activate Notch in endothelial cells (Tg(fli1ep:GAL4FF)ubs3; tg(UAS:NICD)kca3) were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed using the CLC bio Assembly Cell software (version 3.2) and the Ensembl (release 63) predicted cDNAs for the Zv9 genome assembly. qRTM-bM-^@M-^SPCR validation was performed using TaqMan and SYBR Green assays.
2013-09-19 | E-GEOD-41988 | biostudies-arrayexpress
Project description:Methyl tert-butyl ether (MTBE) has been shown to target developing vasculature in piscine and mammalian model systems. In the zebrafish, MTBE induces vascular lesions throughout development. These lesions result from exposure to MTBE at an early stage in development (6-somites to Prim-5 stages). During this time period, transcript levels of vegfa, vegfc, and vegfr1 were significantly decreased in embryos exposed to 5 mM MTBE. We performed global gene analysis as an unbiased approach to discover possible modes of action of MTBE vascular toxicity. Embryos were exposed at 3 hours post fertilization (hpf) in triplicate to one of three concentrations of MTBE: 5mM (induces vascular lesions and significantly decreases vegfa), 0.625mM (NOAEL; no observed adverse effect level), and 0.00625mM (100-fold below NOAEL), or to embryo media (control). Samples were collected at 6-somites (~15hpf), 21-somites (~24 hpf), and Prim-5 (~30 hpf) stages of development. Embryos were meticulously staged at exposure and at the time of collection to maintain a homogeneous population. Our experimental design sought to explore the effect of three concentrations MTBE on three different stages of zebrafish embryonic development during the critical period established for the chemical. This time period also corresponds to an important time in the cardiovascular system develop of our model vertebrate.
2013-09-01 | E-GEOD-46371 | biostudies-arrayexpress
Project description:Human oncogenes involved in the development of hematological malignancies have been widely used to model experimental leukemia. Here, we used the fli1 promoter in zebrafish to target the expression of oncogenic HRAS to endothelial cells, including the hemogenic endothelium and observed the development of a myelo-erythroid proliferative disease. In larvae, the pathological phenotype is characterized by some disruption of the vascular system with prominent expansion of the caudal hematopoietic tissue, increase of expression of stem cell markers and myelo-erythroid specific genes and production of a large number of l-plastin leukocytes. In mosaic juveniles, increased number of hematopoietic blasts and arrest of myeloid maturation was found in kidney marrow. Peripheral blood showed delays of erythrocyte maturation and increased number of circulating myeloid progenitors. We found that the abnormal phenotype is associated with a down regulation of the Notch pathway as shown by the decrease of expression of Notch target genes, whereas overexpressing an activated form of Notch together with the oncogene prevents the expansion of the myelo-erythroid compartment. This study identifies the downregulation of the Notch pathway following an oncogenic event in the hemogenic endothelium as an important step in the pathogenesis of myelo-erythroid diseases and describes a number of potential effectors of this transformation.
2013-09-19 | GSE41988 | GEO
Project description:In order to detect transcriptional differences between primitive and definitive hematopoietic stem and progenitor cells during regular development in the zebrafish embryo, gata1-GFP+/+(18 somites), lmo2-GFP+/+ (18 somites and 35 hpf)1 and cd41-GFP+/+ (35 hpf) cells from transgenic embryos were individually separated from GFP-/- cells by flow cytometry at the indicated stages. For each individual population, pools of 600 - 1500 transgenic embryos were collected. After RNA extraction, labelled cRNA was hybridized onto Affymetrix microarrays. Individual experiments were performed with 2 or 3 biological replicates. Experiment Overall Design: gata1-GFP+/+(18 somites), lmo2-GFP+/+ (18 somites and 35 hpf)1 and cd41-GFP+/+ (35 hpf)2 cells were separated from GFP-/- cells Experiment Overall Design: by flow cytometry at the indicated stages. Sorting was based on propidium iodide exclusion, forward scatter, and GFP Experiment Overall Design: fluorescence, using a FACSVantage flow cytometer (Beckton Dickinson). Sorted cell populations were run twice to optimize cell Experiment Overall Design: purity. Total RNA from cell-sorted populations was extracted with TRIzol reagent (Invitrogen) and purified on RNeasy resins Experiment Overall Design: (Qiagen) according to the manufacturerâs recommendations. Total RNA was subjected to two rounds of linear amplification Experiment Overall Design: (Ambion) and hybridized to Affymetrix zebrafish Gene Chips, according to Affymetrix guidelines. After staining with a Experiment Overall Design: streptavidin-phycoerythrin conjugate (Molecular Probes), the fluorescence of bound RNA was quantitated by using a Gene Chip Experiment Overall Design: scanner (Affymetrix). The raw expression data were calculated and, after pairing of GFP+/+ and GFP-/- samples, statistically Experiment Overall Design: analyzed using methods implemented in Bioconductorâs âaffyâ package and available custom scripts 3,4. Experiment Overall Design: references: Experiment Overall Design: 1. Zhu, H. et al. Regulation of the lmo2 promoter during hematopoietic and vascular development in zebrafish. Dev Biol 281, Experiment Overall Design: 256-69 (2005). Experiment Overall Design: 2. Lin, H. F. et al. Analysis of thrombocyte development in CD41-GFP transgenic zebrafish. Blood 106, 3803-10 (2005). Experiment Overall Design: 3. Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M. & Halfon, M. S. Preferred analysis methods for Affymetrix Experiment Overall Design: GeneChips revealed by a wholly defined control dataset. Genome Biol 6, R16 (2005). Experiment Overall Design: 4. Weber, G. J. et al. Mutant-specific gene programs in the zebrafish. Blood 106, 521-30 (2005).
2008-06-15 | E-GEOD-7658 | biostudies-arrayexpress
Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing.
2014-09-30 | GSE52652 | GEO
Project description:The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells (HSPC) at emergence and initial maturation using scRNA-Seq of enriched blood populations from transgenic fluorescent zebrafish (30 and 52 hpf). Results provide insight into the different HSPC populations in heamtopoietic development.
2021-08-23 | GSE182213 | GEO
Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf
2014-09-30 | E-GEOD-52652 | biostudies-arrayexpress
Project description:We have generated two zebrafish lines carrying inactivating germline mutations in the von Hippel-Lindau (VHL) tumor suppressor gene ortholog vhl. Mutant embryos display a general systemic hypoxic response, including the upregulation of hypoxia-induced genes by 1 day post-fertilization and a severe hyperventilation and cardiophysiological response. vhl mutants develop polycythemia with concomitantly increased epo/epor mRNA levels and Epo signaling. In situ hybridizations reveal global up-regulation of both red and white hematopoietic lineages. Hematopoietic tissues are highly proliferative, with enlarged populations of c-myb+ HSCs and circulating erythroid precursors. Chemical activation of Hif-signaling recapitulated aspects of the vhl-/- phenotype. Furthermore, microarray expression analysis confirms the hypoxic response and hematopoietic phenotype observed in vhl-/- embryos. We conclude that Vhl participates in regulating hematopoiesis and erythroid differentiation. Injections with human VHLp30 and R200W mutant mRNA demonstrate functional conservation of VHL between mammals and zebrafish at the amino acid level, indicating that vhl mutants are a powerful new tool to study genotype-phenotype correlations in human disease. Zebrafish mutants are the first congenital embryonic viable systemic vertebrate animal model for VHL, representing the most accurate model for VHL-associated polycythemia to date. They will contribute to our understanding of hypoxic signaling, hematopoiesis and VHL-associated disease progression.
2009-03-01 | GSE14866 | GEO