Genomics

Dataset Information

40

Trancriptome study of zebrafish mutant fn10a


ABSTRACT: We conducted functional analysis on zebrafish mutant fn10a by polyA+, 100bp paired end, strand-specific RNA-seq. By comparing the transcriptome of fn10a mutants and their wildtype siblings or wildtype controls, we revealed a transcriptome-wide RNA splicing deficiency and a large amount of intron-retaining transcripts, which resulted in compromised nonsense-mediated RNA decay and activation of the p53 pathway in fn10a mutants. 2 biological replicates were performed to consolidate the findings. We also conducted subcellular RNA-seq between fn10a mutants and wildtype siblings, to investigate the localization of intron retaining transcripts. Overall design: The wild-type control group (WT-control group) of 36-hpf embryos was generated from mating crosses between wild-type TL zebrafish, while fn10a mutants (mutant group) and siblings (WT-sibling group) were generated from mating crosses of fn10a heterozygote zebrafish. RNA-seq of 36hpf embryos for fn10a mutants, their wildtype siblings and wildtype TL. RNA-seq of cytoplasm RNA and nuclear RNA from 36hpf embryos for fn10a mutants and their wildtype siblings.

INSTRUMENT(S): Illumina HiSeq 2000 (Danio rerio)

SUBMITTER: Shouyu Yan  

PROVIDER: GSE78106 | GEO | 2017-02-10

SECONDARY ACCESSION(S): PRJNA312615

REPOSITORIES: GEO

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Publications

Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors.

Lei Lei L   Yan Shou-Yu SY   Yang Ran R   Chen Jia-Yu JY   Li Yumei Y   Bu Ye Y   Chang Nannan N   Zhou Qinchao Q   Zhu Xiaojun X   Li Chuan-Yun CY   Xiong Jing-Wei JW  

Nucleic acids research 20170401 6


Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appea  ...[more]

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