Unknown,Transcriptomics,Genomics,Proteomics

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Identification of Transcription Factor F23F12.9::GFP Binding Regions in Embryos

ABSTRACT: modENCODE_submission_3839 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: OP327(official name : OP327 genotype : unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: embryo; Genotype: unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119); Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene F23F12.9; Strain OP327(official name : OP327 genotype : unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: DCC modENCODE

PROVIDER: E-GEOD-48711 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:modENCODE_submission_3371 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: OP343(official name : OP343 genotype : unc119(ed3);wgIs343(C01B12.2:TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The C01B12.2::EGFP fusion protein has broad expression pattern at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs343(C01B12.2:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene C01B12.2; Strain OP343(official name : OP343 genotype : unc119(ed3);wgIs343(C01B12.2:TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The C01B12.2::EGFP fusion protein has broad expression pattern at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

Project description:modENCODE_submission_3217 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: OP215(official name : OP215 genotype : unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The W03F9.2::EGFP fusion protein is mainly expressed in germline cells. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the W03F9.2 transcription factor. made_by : Tony Hyman's lab from MPI-CBG ); Developmental Stage: L4-Young Adult; Genotype: unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L4-Young Adult; Target gene W03F9.2; Strain OP215(official name : OP215 genotype : unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The W03F9.2::EGFP fusion protein is mainly expressed in germline cells. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the W03F9.2 transcription factor. made_by : Tony Hyman's lab from MPI-CBG ); temp (temperature) 20 degree celsius

Project description:modENCODE_submission_4031 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: OP373(official name : OP373 genotype : unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119 outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-67 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene nhr-67; Strain OP373(official name : OP373 genotype : unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119 outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-67 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

Project description:modENCODE_submission_3367 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: OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene C16A3.4; Strain OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

Project description:modENCODE_submission_3370 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: OP339(official name : OP339 genotype : unc119(ed3);wgIs339(nhr-129::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The NHR-129::EGFP fusion protein was expressed in seam cells description : pharynx description : head neurons at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-129 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs339(nhr-129::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-129; Strain OP339(official name : OP339 genotype : unc119(ed3);wgIs339(nhr-129::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. The NHR-129::EGFP fusion protein was expressed in seam cells description : pharynx description : head neurons at L2 stage. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-129 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

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Identification of Transcription Factor F23F12.9::GFP Binding Regions in Embryos

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