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Series GSE8659 Query DataSets for GSE8659
Status Public on Oct 19, 2007
Title Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants
Organism Caenorhabditis elegans
Experiment type Expression profiling by array
Summary 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.
Keywords: Mutant vs. wild type -comparison
 
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).
 
Contributor(s) Asikainen S, Storvik M, Lakso M, Wong G
Citation(s) 17919598
Submission date Aug 02, 2007
Last update date Jul 06, 2016
Contact name Suvi Tuulia Asikainen
E-mail(s) suvi.asikainen@helsinki.fi
Phone +358503311688
Organization name Karolinska Institutet
Department CLINTEC
Lab Outi Hovatta's lab
Street address Karolinska University Hospital
City Stockholm
State/province Huddinge
ZIP/Postal code 14186
Country Sweden
 
Platforms (1)
GPL200 [Celegans] Affymetrix C. elegans Genome Array
Samples (9)
GSM214716 N2 replicate 1
GSM214725 N2 replicate 2
GSM214727 N2 replicate 3
Relations
BioProject PRJNA101859

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8659_RAW.tar 20.0 Mb (http)(custom) TAR (of CEL, CHP)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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