Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of C. elegans young adult hermaphrodites to detect differentially expressed genes in the abscence of lsy-2 activity

ABSTRACT: lsy-2 encodes in C. elegans a C2H2 zinc-finger transcription factor involved in the specification of the left-right asymmetry of the ASE neurons (Johnston and Hobert, 2005) and in the maintenance of germ-soma distinction (Lin et al., 2015). RNA for three different biological replicates was isolated from at least 1000 animals of each genotype: wild type and lsy-2(ot64) and then sequence to detect differentially expressed genes in lsy-2 mutant genotype compared to wild type animals.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: David Rodriguez Crespo

PROVIDER: E-MTAB-14523 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:modENCODE_submission_4812 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: OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene lsy-2; Strain OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

Project description:modENCODE_submission_4813 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: OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs240(lsy-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene lsy-2; Strain OP240(official name : OP240 genotype : unc119(ed3);wgIs240(lsy-2::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 LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

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RNA-seq of C. elegans young adult hermaphrodites to detect differentially expressed genes in the abscence of lsy-2 activity

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