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Association of NUP153 on genomic DNA in TE5 cells [ChIP-seq]

ABSTRACT: Association of NUP153 on genomic DNA in TE5 cells [ChIP-seq]

PROVIDER: PRJNA826342 | ENA |

REPOSITORIES: ENA

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Association of NUP153 on genomic DNA in TE5 cells [ChIP-seq]

Project description:To understand the regulatory regions of genomic DNA by nuclear pore, the genomic region associated by NUP153, one of nuclear pore protein, was determined by Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) .

2023-04-01 | GSE200715 | GEO

Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA

Project description:Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA

| PRJNA932706 | ENA

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress

ChiP-chip profiling of Drosophila melanogaster cell lines to identify targets for nuclear pore proteins Nup153 and Megator.

Project description:ChIP-chip experiment for nuclear pore proteins Nup153 and Mtor in Drosophila S2 and Kc cells. This experiment is related to E-MEXP-2523.

2010-02-12 | E-MEXP-2525 | biostudies-arrayexpress

Genome-wide eNOS-DNA association in Prostate Cancer Cells

Project description:Genome-wide eNOS-DNA association in Prostate Cancer Cells

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Quantitative ChIP-MS analysis of histone modifications present on H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.

2023-12-12 | PXD042224 | Pride

SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability.

Project description:Mutations in SPOP, the gene most frequently point-mutated in primary prostate cancer, are associated with a high degree of genomic instability and deficiency in homologous recombination repair of DNA but the underlying mechanisms. SPOP knockdown leads to spontaneous replication stress and impaired recovery from replication fork stalling. An SPOP interactome analysis shows that wild type (WT) SPOP but not mutant SPOP associates with multiple proteins involved in transcription, mRNA splicing and export. Consistent with the association of SPOP with transcription, splicing and RNA export complexes, the decreased expression of several components of the DNA damage response pathway occurs at the level of transcription.

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High dimensional association detection in large-scale genomic data

Project description:High dimensional association detection in large-scale genomic data

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Organoids-on-a-chip for Colorectal Cancer and in Vitro Screening of Chemotherapeutic Drugs

Project description:The individualized treatment of tumors has always been an urgent problem in clinical practice. Organoids-on-a-chip can reflect the heterogeneity of tumors and is a good model for in vitro anticancer drug screening. In this study, surgical specimens of patients with advanced colorectal cancer will be collected for organoid culture and organoids-on-a- chip. Use organoids-on-a-chip to screen tumor chemotherapy drugs, compare the results of patients’ actual medication regimens, and study the guiding role of organoids in the formulation of precise tumor treatment plans. The investigators will compare the response of organoids to drugs in vitro with the patient’s response to actual chemotherapy and targeted drugs and explore the feasibility and accuracy of organoids-on-a-chip based drug screening for advanced colorectal cancer. The project will establish a screening platform for chemotherapeutic drugs and targeted drugs based on colorectal cancer organoids to quickly and accurately formulate personalized treatment plans for clinical patients.

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