Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of C. elegans dcr-1, unc-32 homozygous mutants vs. coiling unc-32 (wild type) to investidate interference synthesis of small developmental RNAs

ABSTRACT: Homozygous mutant dcr-1 animals were analyzed by Affymetrix microarray analysis using whole worm adult animals. The worms was genetically marked with a recessive allele of unc-32 that exhibits a coiler phenotype in unc-32 homozygous null animals. The "wildtype" comparison worm used in this study were coiling unc-32 animals and the dcr-1 deficient animal contained both the dcr-1 and the unc-32 mutations. Worms were picked and pooled for analysis.
Wormbase concise description of dcr-1 (DiCer Related): The dcr-1 gene encodes a bidentate ribonuclease that is homologous to E. coli RNAse III; dcr-1 is required both for RNA interference and for synthesis of small developmental RNAs; DCR-1 interacts in vivo with RDE-4, a double-stranded RNA (dsRNA) binding protein required for RNAi that interacts with trigger dsRNAs and may function to deliver dsRNAs to DCR-1 for endonucleolytic processing.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Brenda Bass

PROVIDER: E-MEXP-957 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes.

Welker Noah C NC Habig Jeffrey W JW Bass Brenda L BL

RNA (New York, N.Y.) 20070525 7

We describe the first microarray analysis of a whole animal containing a mutation in the Dicer gene. We used adult Caenorhabditis elegans and, to distinguish among different roles of Dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by siRNA, but not miRNA. Surprisingly, we find that the X chromosome is greatly enriched for genes regulated by Dicer. Comparison of all three microarray data sets indicates the majority of Dice ...[more]

PMID: 17526642

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Project description:modENCODE_submission_2430 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP77(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-130::EGFP fusion protein is expressed in the correct unc-130 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-130 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG] official name : OP77 ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene unc-130; Strain OP77(made_by : R. Waterston description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-130::EGFP fusion protein is expressed in the correct unc-130 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-130 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG] official name : OP77 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq

Dataset Information

Transcription profiling of C. elegans dcr-1, unc-32 homozygous mutants vs. coiling unc-32 (wild type) to investidate interference synthesis of small developmental RNAs

Publications

Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes.

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