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E-GEOD-48732 - Snyder_NHR-28_GFP_EMB

Status
Released on 11 July 2013, last updated on 3 June 2014
Organism
Caenorhabditis elegans
Samples (4)
Protocols (1)
Description
modENCODE_submission_4019 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: OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::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 NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ); Developmental Stage: embryo; Genotype: unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene nhr-28; Strain OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::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 NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
Experiment type
ChIP-seq 
Contacts
DCC modENCODE <help@modencode.org>, Anthony Hyman, Ashish Agarwal, Cindie Slightam, Debasish Raha, John Murray, Judi Janette, Mark Gerstein, Mei Zhong, Mihail Sarov, Mike Snyder, Robert Waterston, Stuart Kim, Valerie Reinke, Wei Niu
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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