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TranscriptomicsCoordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention
Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the unde...
ORGANISM(S): Mus musculus 
2012-07-12 | E-GEOD-37933 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant [RNA-seq]
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 intro...
ORGANISM(S): Danio rerio 
2014-02-05 | E-GEOD-53758 | biostudies-arrayexpress
TranscriptomicsSubcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-sequence Retaining Transcripts in Mouse and Rat Neurons.
Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the ne...
ORGANISM(S): Mus musculus 
2013-10-15 | E-GEOD-49592 | biostudies-arrayexpress
ProteomicsMinor intron splicing efficiency increases with the development of lethal prostate cancer
Minor intron-containing genes (MIGs) are crucial cell cycle regulators and are essential for cell survival. Thus, we explored whether MIGs play a role in cancer progression and cancer therapy resistance. Here we show that MIG-expression segregates sensitive and resistant prostate cancer cells from e...
ORGANISM(S): Homo sapiens (Human) 
2023-06-08 | PXD026949 | Pride
Minor spliceosome Lineage plasticity Minor intron genes U6atac Prostate cancer 
TranscriptomicsDetained introns are novel, widespread class of posttranscriptionally-spliced introns
Removal of introns by pre-mRNA splicing is a critical and in some cases rate-limiting step in mammalian gene expression. Deep sequencing of mouse embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within poly(A) selected tran...
ORGANISM(S): Mus musculus 
2015-01-15 | E-GEOD-57231 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of wild type yeast and a mutant deficient for intron degradation using a high density tiling array for genome-wide mapping of introns
High density yeast tiling array reveals new introns and extensive meiotic splicing regulation. Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed an assay for genome-wide ma...
ORGANISM(S): Saccharomyces cerevisiae 
2007-01-29 | E-MEXP-919 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regula...
ORGANISM(S): Arabidopsis thaliana 
2013-02-25 | E-GEOD-41377 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regula...
ORGANISM(S): Arabidopsis thaliana 
2013-02-25 | E-GEOD-41378 | biostudies-arrayexpress
GenomicsIntron retention analysis using isogrowth profiling
Intron retention analysis using isogrowth profiling
PRJNA648363 | ENA
TranscriptomicsNascent-Seq Indicates Widespread Cotranscriptional pre-mRNA Splicing in Drosophila
To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. 87% of introns assayed manifest more than 50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly,...
ORGANISM(S): Drosophila melanogaster 
2011-12-01 | E-GEOD-32950 | biostudies-arrayexpress
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