ArticlePLoS genetics2005
Transcriptome analysis of zebrafish embryogenesis using microarrays.
Article in PLoS genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
What it found
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Who cites it
157 citing papers in PubMed.
- Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish.FEBS open bio · 2026Article
- Dynamic expression of the zebrafish (Danio rerio) proteome across early larval development.Comparative biochemistry and physiology. Part D, Genomics & proteomics · 2025Article
- Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish.bioRxiv : the preprint server for biology · 2025Article
- High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.BMC biology · 2025Article
- Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring.Heredity · 2025Article
- Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes.Bioinformatics and biology insights · 2025Article
- Expression Profiles of Housekeeping Genes and Tissue-Specific Genes in Different Tissues of Chinese Sturgeon (Animals : an open access journal from MDPI · 2024Article
- The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish.The EMBO journal · 2024Article
- Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.Cell reports · 2024Article
- Review
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- A Causal Regulation Modeling Algorithm for Temporal Events with Application toInternational journal of molecular sciences · 2024Article
- Deciphering the function of the fifth class of Gα proteins: regulation of ionic homeostasis as unifying hypothesis.Cellular and molecular life sciences : CMLS · 2024Article
- Tyrosyl-DNA phosphodiesterase 2 (Tdp2) repairs DNA-protein crosslinks and protects against double strand breaksFrontiers in cell and developmental biology · 2024Article
- MCPIP1 functions as a safeguard of early embryonic development.Scientific reports · 2023Article
- Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinksOpen biology · 2023Article
- Actin filaments accumulated in the nucleus remain in the vicinity of condensing chromosomes in the zebrafish early embryo.Biology open · 2023Article
- Maternal mRNA deadenylation and allocation via Rbm14 condensates facilitate vertebrate blastula development.The EMBO journal · 2023Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development.Nucleic acids research · 2022Article
97 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula) revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html).
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Registered trials
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