ChIP_3PEAKS
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002155 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Second batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2
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Project description:This dataset contains data-independent acquisition (DIA) proteomics data generated from K562 human leukemia cells treated with coffee extract or vehicle control. Quantitative proteomic analysis was performed to investigate molecular mechanisms underlying coffee-induced epigenetic remodeling. The proteomics dataset was integrated with histone modification profiling, ChIP-seq and RNA-seq analyses to characterize pathways associated with histone acetylation and MYC transcriptional regulation.
2026-07-08 | PXD080702 | JPOST Repository
Project description:This ChIP-seq dataset examines the genome-wide binding profile of transcription factor MAFB in ovarian cancer cells to investigate its role in tumor progression and immune dysregulation. Using ID8 mouse ovarian cancer cells with MAFB overexpression, we performed chromatin immunoprecipitation followed by high-throughput sequencing to identify MAFB binding sites. Surprisingly, our analysis revealed that IGFBP2, a key mediator of MAFB-driven tumor metastasis and immune modulation, was not a direct transcriptional target of MAFB. The ChIP-seq data was generated using an anti-MAFB antibody, with IgG as control. Peak calling was performed using MACS2 (version 2.2.7.1), and peak annotation was conducted using the ChIPseeker R package. Motif analysis was performed with HOMER (v4.11.1), and differential analysis was conducted with MAnorm.
2025-11-05 | GSE281103 | GEO
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
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Project description:We report the global occupancy by ChIP-seq of AIB1 and TEAD4 in normal mammary epithelial cells (MCF10A). We performed ChIP and library preparation with the ActiveMotif Low Cell ChIP-seq kit. Data was aligned to Hg38 with BWA-MEM, data was sorted and de-duplicated with SAMTOOLS, and peaks were called with MACS2. Analysis was done with ChIP-seeker in R.
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Project description:Embryonic genome activation (EGA) marks the onset of embryonic program and enables the transition toward the first lineage specification. However, the molecular features of EGA and the transcription factors (TFs) orchestrating this process remain unclear. Here, by performing single-cell RNA-seq on bovine embryos, we reveal that major EGA is asynchronously initiated among blastomeres at the 8-cell stage. Integrative analyses reveal distinctive protein accumulation compared to transcription and translation activation during bovine EGA. Furthermore, we investigate the role of SP1, a TF activated at the minor EGA stage, with motifs enriched in accessible chromatin during major EGA stage in bovine and human embryos. SP1 deficiency leads to morula arrest in bovine and impairs EGA in human embryos. Multi-omics analysis demonstrates that SP1 promotes early lineage gene expression by modulating nearby chromatin states in bovine and directly targets key EGA genes in human embryos. Together, our study delineates the dynamics of bovine EGA and uncovers the conserved and species-specific roles of SP1 in regulating EGA and early development in mammals.
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