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E-GEOD-25927 - Genome-wide analysis of alternative splicing in Caenorhabditis elegans

Status
Released on 14 December 2010, last updated on 26 June 2012
Organism
Caenorhabditis elegans
Samples (5)
Array (1)
Protocols (6)
Description
Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provides the most comprehensive set of annotated splice variants in C. elegans to date, and is therefore expected to faciliate focused, high resolution in vivo functional assays of AS function. Alternative splicing events were identified from alignments of C. elegans mRNA/EST sequences (UniGene Build #26) to C. elegans genomic sequence (NCBI timestamp: Sept. 25, 2006), essentially as previously described (Pan et al. 2005; Pan et al. 2004). In total, 499 cassette type AS events were identified. For each AS event, 3 exon probes and 3 exon junction probes were designed to profile the AS event on the microarray, essentially as previously described (Pan et al. 2004). This submission represents the expression microarray component of the study.
Experiment type
transcription profiling by array 
Contacts
Qun Pan <qun.pan@utoronto.ca>, Andrew C Nelson, Andrew G Fraser, Arun K Ramani, Benjamin J Blencowe, John A Calarco, Leo J Lee, Mei Zhen, Quaid Morris, Sepand Mavandadi, Ying Wang
Citation
Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG. , PMID:21177968
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-25927.idf.txt
Sample and data relationshipE-GEOD-25927.sdrf.txt
Processed data (1)E-GEOD-25927.processed.1.zip
Additional data (2)E-GEOD-25927.additional.1.zip, E-GEOD-25927.additional.2.zip
Array designA-GEOD-11296.adf.txt
Links