E-GEOD-13258 - Transcription profiling of C. elegans L1-L2 stage nematodes wild type and four mutants (alg-1, zfp-1, rde-4, lin-35)

Status
Submitted on 17 October 2008, released on 13 January 2009, last updated on 10 June 2011
Organism
Caenorhabditis elegans
Samples (15)
Array (1)
Protocols (5)
Description
Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. Based on this microarray analysis of gene expression in RNA interference (RNAi)-related mutants rde-4, zfp-1 and alg-1 and the Retinoblastoma (Rb) mutant lin-35, we found that a component of Dicer complex RDE-4 and a chromatin-related zinc finger protein ZFP-1, not implicated previously in endogenous RNAi, regulate overlapping sets of genes. Notably, genes a) upregulated in the rde-4 and zfp-1 mutants and b) upregulated in the lin-35(Rb) mutant, but not the downregulated genes are highly represented in the set of genes with corresponding endogenous short interfering RNAs (endo-siRNAs). Experiment Overall Design: Nematodes were synchronized at L1 stage for RNA preparations. All conditions (WT and 4 mutants) were profiled in triplicate. Replicates were biological replicates (separately grown worm populations), with two exceptions: due to shortage of biological material available for the lin-35(n745) unc-13(e1091) I and zfp-1(ok554) III strains, one of the two biological samples was hybridized twice in order to set up a consistent triplicate structure across the dataset.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-13258.idf.txt
Sample and data relationshipE-GEOD-13258.sdrf.txt
Raw data (1)E-GEOD-13258.raw.1.zip
Processed data (1)E-GEOD-13258.processed.1.zip
Array designA-AFFY-60.adf.txt
R ExpressionSetE-GEOD-13258.eSet.r
Links