Lin-35(n745) mutants vs. lin-35(n745), mes-4(RNAi) (below referred to as reference sample and test sample respectively)
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Andreas Rechtsteiner
PROVIDER: E-GEOD-26825 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and lin-35(n745) treated with mes-4(RNAi) at 26 degrees.
2011-01-25 | GSE26825 | GEO
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and N2 (wild type) at 26 degrees. One-condition experiment, mutant (lin-35) vs. WT. Biological replicates 4 mutant, 4 wildtype harvested indepedently. One lin-35 replicate and one WT replicate per array.
2011-01-25 | E-GEOD-26824 | biostudies-arrayexpress
Project description:Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and N2 (wild type) at 26 degrees.
2011-01-25 | GSE26824 | GEO
Project 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.
2009-01-13 | E-GEOD-13258 | biostudies-arrayexpress
Project description:lin-35(n745) mutants vs. lin-35(n745), mes-4(RNAi) (below referred to as reference sample and test sample respectively)
| PRJNA136029 | ENA
Project description:modENCODE_submission_3213 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: YL409(official name : YL409 genotype : unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by its own lin-35 promoter. made_by : Michelle Kudron (Valerie Reinke's lab) ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene lin-35; Strain YL409(official name : YL409 genotype : unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by its own lin-35 promoter. made_by : Michelle Kudron (Valerie Reinke's lab) ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48697 | biostudies-arrayexpress
Project description:modENCODE_submission_3602 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: YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene lin-35; Strain YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius
2013-02-04 | E-GEOD-44015 | biostudies-arrayexpress
Project description:modENCODE_submission_3603 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: YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene lin-35; Strain YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius
2013-02-04 | E-GEOD-44016 | biostudies-arrayexpress
Project description:LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in conjunction with E2F. In addition, LIN-35 was found to regulate neuronal genes during embryogenesis and targets of the intestinal-specific GATA transcription factor, ELT-2, at multiple developmental stages. Additional findings suggest that LIN-35 functions in cell cycle regulation in embryos in a manner that is independent of E2F. A comparison of LIN-35-regulated genes with known fly and mammalian pocket-protein targets revealed a high degree of overlap, indicating strong conservation of pocket protein functions in diverse phyla. Based on microarray results and our refinement of the C. elegans E2F consensus sequence, we were able to generate a comprehensive list of putative E2F-regulated genes in C. elegans. These results implicate a large number of genes previously unconnected to cell cycle control as having potential roles in this process. Experiment Overall Design: We compared transcriptom profiles of lin-35 mutants and control N2 worms at 3 developmental stages (embryonic, L1 and L4). Experiment Overall Design: Each comparison was done in triplicate on independently grown and isolated animals.
2008-06-14 | E-GEOD-6547 | biostudies-arrayexpress
Project description:modENCODE_submission_3833 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: YL468(official name : YL468 genotype : unc-119(ed3) III; vrIs93 [pMEX-5::LIN-35:GFP:FLAG::LIN-35 3-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : LIN-35 expressed under the germline-specific promoter MEX-5. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; vrIs93 [pMEX-5::LIN-35:GFP:FLAG::LIN-35 3-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene lin-35; Strain YL468(official name : YL468 genotype : unc-119(ed3) III; vrIs93 [pMEX-5::LIN-35:GFP:FLAG::LIN-35 3-UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : LIN-35 expressed under the germline-specific promoter MEX-5. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48705 | biostudies-arrayexpress