Chromatin immunoprecipitation of C. elegans intestine
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Janos Demeter
PROVIDER: E-SMDB-3592 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans.
Pauli Florencia F Liu Yueyi Y Kim Yoona A YA Chen Pei-Jiun PJ Kim Stuart K SK
Development (Cambridge, England) 20051214 2
We used mRNA tagging to identify genes expressed in the intestine of C. elegans. Animals expressing an epitope-tagged protein that binds the poly-A tail of mRNAs (FLAG::PAB-1) from an intestine-specific promoter (ges-1) were used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine. A total of 1938 intestine-expressed genes (P<0.001) were identified using DNA microarrays. First, we compared the intestine-expressed genes with those expressed in the muscle and germline, and identifie ...[more]
Similar Datasets
Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab Set of arrays that are part of repeated experiments Keywords: Biological Replicate, mRNA tagging
2006-02-03 | GSE4150 | GEO
Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab Set of arrays that are part of repeated experiments Biological Replicate Computed
2006-02-02 | E-GEOD-4150 | biostudies-arrayexpress
Project description:mRNA tagging in the intestine of C. elegans. FLAG::PAB-1 was expressed from the intestine-specific promoter for ges-1 and used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine with anti-FLAG antibody on agarose beads. This mRNA was amplified, cDNA was synthesized and labeled with Cy5. Total RNA from the same strain, but without the IP was amplified and cDNA was synthesized and labeled with Cy3. These two samples were compared on C. elegans DNA printed arrays from the Stuart Kim lab. 1938 intestine-expressed genes were identified (p<0.001) after eight repeats of the experiment A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Type = replicate_design Series_overall_design: Computed Keywords: other
2005-12-20 | GSE2626 | GEO
Project description:mRNA tagging in the intestine of C. elegans. FLAG::PAB-1 was expressed from the intestine-specific promoter for ges-1 and used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine with anti-FLAG antibody on agarose beads. This mRNA was amplified, cDNA was synthesized and labeled with Cy5. Total RNA from the same strain, but without the IP was amplified and cDNA was synthesized and labeled with Cy3. These two samples were compared on C. elegans DNA printed arrays from the Stuart Kim lab. 1938 intestine-expressed genes were identified (p<0.001) after eight repeats of the experiment A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Type = replicate_design Series_overall_design: Computed
2010-06-05 | E-GEOD-2626 | biostudies-arrayexpress
Project description:modENCODE_submission_3834 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: YL474(official name : YL474 genotype : lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and expressed in the intestine. The original transgene was subsequently crossed into a lin-35 mutant. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: starved L1; Genotype: lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage starved L1; Target gene lin-35; Strain YL474(official name : YL474 genotype : lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and expressed in the intestine. The original transgene was subsequently crossed into a lin-35 mutant. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48706 | biostudies-arrayexpress
Project description:modENCODE_submission_3210 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: YL448(official name : YL448 genotype : unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG: DPL-1 3'UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag made_by : Michelle Kudron (Valerie Reinke's lab) ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG: DPL-1 3'UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene dpl-1; Strain YL448(official name : YL448 genotype : unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG: DPL-1 3'UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag made_by : Michelle Kudron (Valerie Reinke's lab) ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48696 | biostudies-arrayexpress
Project description:modENCODE_submission_3601 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: OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 tags : Bombard tag : GFP::3xFlag 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite; Transgene: sptf-1; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene sptf-1; Strain OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 tags : Bombard tag : GFP::3xFlag 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius
2013-02-04 | E-GEOD-44014 | biostudies-arrayexpress
Project description:modENCODE_submission_3604 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: YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::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; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene hpl-2; Strain YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::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-44017 | biostudies-arrayexpress
Project description:modENCODE_submission_3211 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: YL418(official name : YL418 genotype : unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The EFL-1::GFP fusion protein is driven by the ges-1 promoter and expressed in the instestine. made_by : Michelle Kudron (Valerie Reinke's lab) ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene efl-1; Strain YL418(official name : YL418 genotype : unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The EFL-1::GFP fusion protein is driven by the ges-1 promoter and expressed in the instestine. made_by : Michelle Kudron (Valerie Reinke's lab) ); temp (temperature) 20 degree celsius
2014-04-10 | E-GEOD-56707 | 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