ArticleBMC developmental biology2011
The zebrafish transcriptome during early development.
Article in BMC developmental biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed, 134 citations in OpenAlex.
- Lampbrush chromosomes of Danio rerio.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Maternal provisioning and zygotic activation: transcriptomic dynamics of early atlantic halibut (Frontiers in cell and developmental biology · 2025Article
- Systematic Identification of Long Noncoding RNAs during Three Key Organogenesis Stages in Zebrafish.International journal of molecular sciences · 2024Article
- Single-nucleus chromatin landscapes during zebrafish early embryogenesis.Scientific data · 2023Article
- Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein-Nucleotide Interactions in Zebrafish Embryos.ACS chemical biology · 2023Article
- High-throughput transcriptome sequencing reveals the key stages of cardiovascular development in zebrafish embryos.BMC genomics · 2022Article
- Eomes function is conserved between zebrafish and mouse and controls left-right organiser progenitor gene expression via interlocking feedforward loops.Frontiers in cell and developmental biology · 2022Article
- Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages.BMC genomics · 2021Article
- Developmental and Neurotoxicity of Acrylamide to Zebrafish.International journal of molecular sciences · 2021Article
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- PLK1- and PLK4-Mediated Asymmetric Mitotic Centrosome Size and Positioning in the Early Zebrafish Embryo.Current biology : CB · 2020Article
- Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (International journal of molecular sciences · 2020Article
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- Article
- Tissue-Specific Requirement for the GINS Complex During Zebrafish Development.Frontiers in cell and developmental biology · 2020Article
- Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis).BMC genomics · 2019Article
- Induction of interferon-stimulated genes and cellular stress pathways by morpholinos in zebrafish.Developmental biology · 2019Article
- Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes.Human molecular genetics · 2019Article
- Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (G3 (Bethesda, Md.) · 2019Article
- Early Developmental Zebrafish Embryo Extract to Modulate Senescence in Multisource Human Mesenchymal Stem Cells.International journal of molecular sciences · 2019Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized. In this study RNA-Seq is used to compare the transcription profiles of four early developmental stages in zebrafish (Danio rerio) on a global scale.
resultsAn average of 79 M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187, of which 10096 were present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. The sequence data (accession number ERP000635) is available at the European Nucleotide Archive.
conclusionClustering of expression profiles shows that a majority of the detected gene transcripts are present at steady levels, and thus a minority of the gene transcripts clusters as increasing or decreasing in expression over the four investigated developmental stages. The three earliest developmental stages were similar when comparing highly expressed genes, whereas the 50% epiboly stage differed from the other three stages in the identity of highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions. Taken together, these observations indicate a major transition in gene regulation and transcriptional activity taking place between the 512-cell and 50% epiboly stages, in accordance with previous studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.