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MRNA sequencing time course of C. elegans samples at time point 1 hours until time point 24 hours at 25 degree [blmp-1(tm548) mutant]

ABSTRACT: We find gene expression oscillations which arise after a time lag of around 5 hours. Molecular oscillators can organize gene expression during development both temporally and spatially. In C. elegans, oscillations occur for ~25% of the transcriptome to control molting and potentially other developmental processes. The underlying mechanisms and organization of the oscillator remain unknown. We investigated the transcription factor BLMP-1, orthologous to mammalian PRDM1, as a rhythmically accumulating transcription factor that is required for robust rhythmic development, molting, and animal viability. We have sequenced synchronously growing populations of wild-type and blmp-1(tm548) mutant animals in a time course from 1 – 24 hours after plating with an hourly resolution.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE147388 | GEO | 2020/07/27

REPOSITORIES: GEO

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Project description:modENCODE_submission_2612 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: OP109(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 BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] official name : OP109 ); Developmental Stage: fed L1; Genotype: unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene blmp-1; Strain OP109(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 BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] official name : OP109 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq

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MRNA sequencing time course of C. elegans samples at time point 1 hours until time point 24 hours at 25 degree [blmp-1(tm548) mutant]

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