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Quantitative microarray profiling of alternative splicing in mouse tissues

ABSTRACT: We describe the application of a new microarray platform, which combines information from exon body and splice-junction probes, to analyze the regulation of 3126 alternative splicing events in ten mouse tissues. The details of the methods and algorithms are described in this paper: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform (Molecular Cell, Dec., 2004) Keywords = A new quantitative alternative splicing microarray platform Keywords: other

ORGANISM(S): Mus musculus

PROVIDER: GSE2054 | GEO | 2004/12/22

SECONDARY ACCESSION(S): PRJNA91715

REPOSITORIES: GEO

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Quantitative microarray profiling of alternative splicing in mouse tissues

Project description:We describe the application of a new microarray platform, which combines information from exon body and splice-junction probes, to analyze the regulation of 3126 alternative splicing events in ten mouse tissues. The details of the methods and algorithms are described in this paper: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform (Molecular Cell, Dec., 2004) Keywords = A new quantitative alternative splicing microarray platform

2010-05-27 | E-GEOD-2054 | biostudies-arrayexpress

Functional coordination of alternative splicing in the mammalian central nervous system

Project description:Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues. Keywords: Alternative splicing

2007-08-01 | GSE8081 | GEO

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

Project description:We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels. Keywords: mRNA expression 32-nucleotide sequence reads from six human tissues including brain, cerebral cortex, heart, liver, lung and skeletal muscle.

2008-11-19 | E-GEOD-13652 | biostudies-arrayexpress

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

2008-11-19 | GSE13652 | GEO

Mus musculus

Project description:Quantitative microarray profiling of alternative splicing in mouse tissues

| PRJNA91715 | ENA

PBMCs from CCI-779 Treated RCC subjects

Project description:Clinical Pharmacogenomics study. Renal Cell Carcinoma subjects were treated with CCI-779 and peripheral blood mononuclear cells were profiled over time of treatment. Population pharmacokinetics of CCI-779: Correlations to safety and pharmacogenomics responses in patients with advanced renal cancer. Clin Pharm Therapeutics Dec 2004 Keywords: other

2004-12-01 | GSE1982 | GEO

Analysis of gene expression in rice mature leaf and cultured cell suspension using Rice SuperSAGE Array1

Project description:We developed a novel platform for genome-wide gene expression analysis in any eukaryotic organism, that we coin SuperSAGE Array. The SuperSAGE Array is a microarray onto which oligonucleotides of 26 nucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE Array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. Highly reproducible gene expression profiling by the SuperSAGE Array was demonstrated for a thousand of genes (tags) in rice. Keywords: Tissues, SuperSAGE, 26base oligonucleotide

2006-07-28 | GSE4685 | GEO

MicroRNA expression patterns in mouse tissues and staged embryos

Project description:RNA from seven adult mouse tissues, four staged whole mouse embryos, ES cells, 3 day and 28 day embryoid bodies was profiled against the microRNA microarray. A custom microarray platform for analysis of microRNA gene expression; Nature Methods 1, 47 - 53 (2004) Keywords = microRNA Keywords = miRNA Keywords: other

2004-09-02 | GSE1635 | GEO

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (expression)

Project description:The rate of RNA polymerase II (pol II) elongation can influence splice site selection in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing is not well understood. We performed experiments to perturb pol II elongation and then globally compared alternative splicing patterns with genome-wide pol II occupancy. RNA binding and RNA processing functions were significantly enriched among the genes with pol II elongation inhibition-dependent changes in alternative splicing. Under conditions that interfere with pol II elongation, including cell stress, increased pol II occupancy was detected in the intronic regions flanking the alternative exons in these genes, and these exons generally became more included. A disproportionately high fraction of these exons introduced premature termination codons that elicited nonsense-mediated mRNA decay (NMD), thereby further reducing transcript levels. Our results provide evidence that kinetic coupling between transcription, alternative splicing and NMD affords a rapid mechanism by which cells can respond to changes in growth conditions, including cell stress, to coordinate the levels of RNA processing factors with mRNA levels. In order to identify alternative splicing events influenced by changes in pol II elongation, we performed quantitative alternative splicing microarray profiling (Pan et al., 2004 (PMID 15610736); Shai et al., 2006 (PMID 16403798)) of RNA isolated from stimulated Jurkat T lymphoma cells, cultured separately in the presence or absence of two different drugs that can inhibit pol II elongation: 5,6-dichloro-1-β-D-ribofuranosyl-benzimidazole (DRB) and camptothecin.

2010-12-09 | E-GEOD-25287 | biostudies-arrayexpress

Determining the impact of alternative splicing events on transcriptome dynamics

Project description:Background The complete sequencing of the human genome and its subsequent analysis revealed a predominant role for alternative splicing in the generation of proteome diversity. Splice switching oligonucleotides (SSOs) are a powerful and specific tool to experimentally control alternative splicing of endogenous messenger RNAs in living cells. SSOs also have therapeutic potential to treat diseases that are caused by aberrant splicing. The assignment of biological roles to alternative splicing events of currently unknown function promises to provide a largely untapped source of potential new therapeutic targets. Here we have developed a protocol that combines high sensitivity microarrays with the transfection of SSOs to monitor global changes in gene expression downstream of alternate, endogenous splice events. Findings When applied to a well-characterized splicing event in the Bcl-x gene, the application of high sensitivity microarrays revealed a link between the induction of the Bcl-xS isoform and the repression of genes involved in protein synthesis. Conclusions The strategy introduced herein provides a useful approach to define the biological impact of any given alternative splicing event on global gene expression patterns. Furthermore, our data provide the first link between Bcl-xS expression and the repression of ribosomal protein gene expression. Biological triplicates, 2 conditions: control oligonucleotide, Bcl-x oligonucleotide

2008-10-02 | E-GEOD-9851 | biostudies-arrayexpress

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