Transcriptomics

Dataset Information

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Genome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant [RNA-seq]


ABSTRACT: To determine the global impact of the clbn mutation on gene expression and efficiency of U2- and U12-type splicing, we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2-type and U12-type intron on a genome-wide scale to confirm that rnpc3 deficiency specifically impairs U12-type splicing. RNAseq and microarray data were combined to yield high-confidence lists of differentially expressed genes which show that impaired U12-type splicing has a wide-ranging effect on the developing transcriptome. RNAseq libraries prepared from 108 hours post-fertilization zebrafish larvae (approx. 60 embryos each, genotyped homozygous wildtype and homozygous clbns841 mutants, respectively)

ORGANISM(S): Danio rerio  

SUBMITTER: Annie Y Ng   Karen Doggett  Andrew J Trotter  Maria-Cristina Keightley  Rea M Lardelli  Simon J Wilkins  Sean M Grimmond  Joan K Heath  Didier Y Stainier  Sebastian Markmiller  Joan Kathleen Heath  Elke A Ober  Graham J Lieschke  Nicole Cloonan  Heather Verkade  Holly A Field  Yeliz Boglev 

PROVIDER: E-GEOD-53758 | ArrayExpress | 2014-02-05

SECONDARY ACCESSION(S): GSE53758SRP035264PRJNA236557

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating ge  ...[more]

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