Transcriptomics

Dataset Information

3

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


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. Total RNA was prepared from pools consisting of approx. 20 individually genotyped homozygous wildtype or mutant larvae, respectively. Three biologically independent replicate pools were generated and analyzed for each condition.

ORGANISM(S): Danio rerio  

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

PROVIDER: E-GEOD-53934 | ArrayExpress | 2014-02-05

SECONDARY ACCESSION(S): GSE53934PRJNA236231

REPOSITORIES: GEO, ArrayExpress

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