Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377902 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The exon junction complex (EJC) is composed of three core proteins Rbm8a, Magoh and Eif4a3 and is thought to play a role in several post-transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome-wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing (RIP-Seq). We find that, as in human cells, zebrafish EJC is deposited about 24 nts upstream of exon-exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA-seq from rbm8a mutant, magoh mutant and wild-type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants.
2019-07-30 | GSE135019 | GEO
Project description:This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish (Danio rerio). Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24, 36, 72 and 96 hrs post fertilization, embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish.
2012-10-15 | GSE41373 | GEO
Project description:we determined the contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish embryos by overexpressing a dominant-negative form of Dcp2.
2017-05-31 | GSE95679 | GEO
Project description:Quantitative analysis of thyroid response in zebrafish embryos
| PRJNA131189 | ENA
Project description:This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish (Danio rerio). Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24, 36, 72 and 96 hrs post fertilization, embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Catecholaminergic neurons were labeled by four different strategies: (1) 24 hrs old embryos: we used the ETvmat2:GFP transgenic line (Wen et al. 2007). Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84-92) which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; (2) 24 hrs old embryos: we used Tg(otpb.A:egfp)zc48 transgenic line (Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011, Vol 352, p393–404) which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. (3) For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons (Tay et al., Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2, 171; also: T. Leng and W. Driever, unpublished). (4) for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells (Fernandes et al., Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22 DOI 10.1016/j.cub.2012.08.016). We used the different transgenic lines, because lines (3) and (4) do not efficiently label catecholaminergic neurons at early stages, while lines (1) and (2) also have GFP expression in several other non-catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP-tagged zebrafish (Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633). RNA was either processed for NanoCAGE, or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA-Seq depth: Samples 1-4 (NanoCage): Samples 5-8 (RNA-Seq high read numbers), and SAmples 9-12 (RNA-Seq low read numbers).
2012-10-15 | E-GEOD-41373 | biostudies-arrayexpress
Project description:Purpose:To investigate the transcriptomic profiles in zebrafish embryos exposed externally to nucleotides at a critical develpomental window (3-7 days post fertilization) determine biological processes and pathways based on differentially expressed gene transcripts using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 7 dpf zebraifsh embryos after exposure to 10-5M ATP, AMP, adenosine and adenine were generated by deep sequencing, in triplicate, using Illumina HiSeq2500 Results: There were many differentially expressed genes; including ubiquitin-, actin-, and tubulin-related, showing that the cytoskeleton was altered; other DEGs involved with purine binding, specifically guanine, which was expected as the mixture was composed of purines; DEGs involved with GTP binding were also upregulated, suggesting increased cell signaling,
2020-03-23 | GSE97016 | GEO