ChIP-seq of UNC-30 and UNC-55 in C.elegans
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE102213 | GEO | 2017/08/28
SECONDARY ACCESSION(S): PRJNA397009
REPOSITORIES: GEO
Similar Datasets
Project description:We performed ChIP-seq on endogenously tagged UNC-3::GFP fusion proteins in C. elegans
2020-10-01 | GSE143165 | GEO
Project description:Purpose: To uncover immune and longevity genes and pathways that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling in C elegans Methods: RNA was extracted from synchronized L4 stage unc-30(ok613) and WT animals grown at 20 C using Qiagen extraction kits and following standard methods Results: RNA seq analyses shows enriched and signficant upregulated immune, neuropeptide, ageing and metabolism genes and pathways that are dependent of GABAergic signaling Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans
2021-05-05 | GSE149742 | GEO
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
2011-02-18 | E-GEOD-25783 | biostudies-arrayexpress
Project description:modENCODE_submission_3254 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: OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene unc-62; Strain OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29471 | biostudies-arrayexpress
Project description:modENCODE_submission_3222 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: OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene unc-62; Strain OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29468 | biostudies-arrayexpress
Project description:modENCODE_submission_3375 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: OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene unc-62; Strain OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29475 | biostudies-arrayexpress
Project description:modENCODE_submission_3584 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: OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); Developmental Stage: Day Four Young Adult; Genotype: unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Day Four Young Adult; Target gene unc-62; Strain OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : 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 UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius
2012-06-04 | E-GEOD-38436 | biostudies-arrayexpress
Project description:Purpose: To uncover immune mediated genes and pathways by Pseudomonas aeruginosa infection that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling in C. elegans Methods: RNA was extracted from synchronized Pseudomonas aeruginosa infected L4 stage unc-30(ok613) and WT using Qiagen extraction kits and following standard methods. The animals were grown on OP50 at 20 C and infected at 25 C. Results: RNA seq analyses shows enriched and signficant Pseudomonas aeruginosa mediated upregulated immune, neuropeptide and metabolism genes and pathways that are dependent of GABAergic signaling Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans during Pseudomonas aeruginosa infection
2021-01-31 | GSE149862 | GEO
Project description:modENCODE_submission_2620 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: OP120(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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); Developmental Stage: late embryo; Genotype: unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene ceh-30; Strain OP120(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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25808 | biostudies-arrayexpress
Project description:modENCODE_submission_4035 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: NC1639(official name : NC1639 genotype : [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross : 0 mutagen : None tags : GFP description : Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA motor neurons (also some ectopic expression in other cells). This line is integrated and shows strong GFP expression. made_by : David Miller lab ); Developmental Stage: L2; Genotype: [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene unc-55; Strain NC1639(official name : NC1639 genotype : [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross : 0 mutagen : None tags : GFP description : Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA
2013-07-11 | E-GEOD-48742 | biostudies-arrayexpress