Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression analysis of blastocysts in Kdm4b-PEs

ABSTRACT: To identify the genes that are controled by H3K9me3 modification in PEs, we conducted transcriptome analysis using Egfp-, Kdm4b-PEs, and IVF embryos at blastocyst stages. Kdm4b or Egfp mRNA injected oocytes were parthenogenetically activated. IVF embryos were generated according to standard protcol. All embryos were cultured in KSOM medium for 120 hours after activation or sperm insemination. Five blastocysts per one biological replicate were pooled and analyzed.

ORGANISM(S): Mus musculus

SUBMITTER: Atsushi Fukuda

PROVIDER: E-GEOD-53662 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice.

Fukuda Atsushi A Tomikawa Junko J Miura Takumi T Hata Kenichiro K Nakabayashi Kazuhiko K Eggan Kevin K Akutsu Hidenori H Umezawa Akihiro A

Nature communications 20141114

Maintaining a single active X-chromosome by repressing Xist is crucial for embryonic development in mice. Although the Xist activator RNF12/RLIM is present as a maternal factor, maternal Xist (Xm-Xist) is repressed during preimplantation phases to establish imprinted X-chromosome inactivation (XCI). Here we show, using a highly reproducible chromatin immunoprecipitation method that facilitates chromatin analysis of preimplantation embryos, that H3K9me3 is enriched at the Xist promoter region, pr ...[more]

PMID: 25394724

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Project description:modENCODE_submission_3157 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: OP87 (official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG] 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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene pes-1; Strain OP87 (official name : OP87 genotype : unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG] 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 PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

Dataset Information

Expression analysis of blastocysts in Kdm4b-PEs

Publications

The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice.

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