E-GEOD-8659 - Transcription profiling of C. elegans rrf-3 and eri-1 mutants

Status
Submitted on 2 August 2007, released on 16 June 2008, last updated on 2 May 2014
Organism
Caenorhabditis elegans
Samples (9)
Array (1)
Protocols (8)
Description
RRF-3 and ERI-1 are first identified proteins required for accumulation of at least some endogenous secondary siRNAs in C.elegans. Genome wide gene expression analysis was performed on L4 stage rrf-3 and eri-1 mutant C. elegans to study effects caused by loss of these proteins. Mutant rrf-3 and eri-1 strains exhibited similar expression patterns when compared to N2 wild type, while 72 transcripts were found to be co-overexpressed and 4 transcripts co-underexpressed (> 2-fold, p< 0.05). Ontology analysis indicated many of the gene products were associated with protein phosphorylation and sperm function. These results provide additional support for the hypothesis that RRF-3 and ERI-1 act together in a siRNA pathway and may indicate biological processes that are related to endo-siRNAs. Experiment Overall Design: rrf-3(pk1426) mutant worms (NL2099), eri-1 (mg366) mutant worms (GR1373), and wild type worms (N2) were grown on culturing plates containing NGM agar media with OP50 Escherichia coli (E. coli). Worms were grown at 20°C and harvested at L4 stage. RNA isolation was made using Ribopure Total RNA isolation -kit (Ambion). Animals were grown and RNA isolated separately for each biological replicate. Total RNA was labeled for chip experiments using the cRNA protocol (Affymetrix, Palo Alto, CA). DNA from each mutant was hybridized to Gene Chip C. elegans whole genome arrays containing 22,500 transcripts (Affymetrix, Palo Alto, CA) as three biological replicates (3 chips each for N2, rrf-3, eri-1). Microarray hybridization and scanning was performed at the Biomedicum Biochip Center (Helsinki, Finland).
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants. Suvi Asikainen, Markus Storvik, Merja Lakso, Garry Wong. FEBS Lett 581(26):5050-4 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-8659.idf.txt
Sample and data relationshipE-GEOD-8659.sdrf.txt
Raw data (1)E-GEOD-8659.raw.1.zip
Processed data (1)E-GEOD-8659.processed.1.zip
Array designA-AFFY-60.adf.txt
R ExpressionSetE-GEOD-8659.eSet.r
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