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| 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
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| 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
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| 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).
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| 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
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| Organization name |
Karolinska Institutet
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| Department |
CLINTEC
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| Lab |
Outi Hovatta's lab
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| Street address |
Karolinska University Hospital
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| City |
Stockholm |
| State/province |
Huddinge |
| ZIP/Postal code |
14186 |
| Country |
Sweden |
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| Platforms (1) |
| GPL200 |
[Celegans] Affymetrix C. elegans Genome Array |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA101859 |
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