MRNA-seq analysis of Caenorhabditis elegans daf-18(ok480) and WT starved L1 larvae shortly after hatching
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE151299 | GEO | 2021/06/21
REPOSITORIES: GEO
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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
Project description:This project includes two proximity labeling experiments, one to establish the vicinity of UNC-45 under non-stress conditions and one to examine changes in the vicinity of UNC-45 under optogenetically induced mechanical muscle stress. The first non-stress experiment consists of 15 samples after biotin-streptavidin pull-down in 5 replicates of 3 conditions (3 transgenic C. elegans strains). Transgenic C. elegans strains expressing the mutant BirA biotin ligases miniTurbo and TurboID in body wall muscle cells were used to compare a proximity-labeled strain expressing an UNC-45-miniTurbo-2xHA fusion protein in the muscle cells (PP3135 unc-119(ed4)III; hhIs241[unc-54p::unc-45::miniTurbo::2xHA; unc-119(+)]) with a strain expressing the biotin ligase TurboID-2xHA without fusion protein in muscle cells (PP3138 unc-119(ed4)III; hhIs242[unc-54p::TurboID::2xHA; unc-119(+)]) to find transient interactors of the myosin chaperone UNC-45 in muscle. As a control, we included a strain expressing a transgenic UNC-45-FLAG protein in the body wall muscle (PP1017 unc-119(ed4)III; hhIs84[unc-119(+); unc-54p::unc-45::FLAG]). Biotinylated proteins in 2.5 mg lysates of these strains were pulled down with streptavidin sepharose beads and identified by mass spectrometry. The second mechanical stress experiment consists of 10 samples after biotin-streptavidin pull-down in 5 replicates of 2 conditions. A transgenic C. elegans strain expressing the biotin ligase miniTurbo fused to UNC-45 in body wall muscle cells was crossed with a transgenic strain expressing the optogenetic channelrhodopsin mutant ChR2(C128S;H134R)-FLAG in body wall muscle cells (PP3358 hhIs241[unc-54p::unc-45::miniTurbo::2xHA; unc-119(+)]; hhIs251[myo-3p::ChR2(C128S,H134R)-FLAG::unc-54 3'UTR, Cbrunc-119(+)]). The latter transgene is used to contract the worms’ muscles by blue light illumination to induce mechanical muscle stress. The optogenetic channel is activated by adding the cofactor all-trans retinal (ATR) to its food source E. coli OP50. In this experiment, we compared proximity-labeling in the UNC-45-miniTurbo-2xHA expressing strain under conditions with ATR (L+, treatment, contraction) with proximity-labeling in the UNC-45-miniTurbo-2xHA expressing strain under conditions without ATR (L-, control, no contraction) to find transient interactors of the candidate UNC-45 in muscle under mechanical stress. Biotinylated proteins in 2.5 mg of lysates of these strains were pulled down using streptavidin sepharose beads and identified by mass spectrometry.
2024-07-16 | PXD045081 | Pride
Project description:modENCODE_submission_3075 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: YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene dpl-1; Strain YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37802 | 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_4641 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: YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene hpl-2; Strain YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius
2013-11-01 | E-GEOD-51983 | 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_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
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