Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq analysis of MBD3 in human breast cancer cells

ABSTRACT: Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful approach to identify the genome-wide localization of protein of interest. However, to perform ChIP-seq experiments for large protein complex, such as Mi-2/NuRD complex, is still challenging. Here, we present high-quality MBD3 ChIP-seq data in human breast cancer cells, MDA-MB-231. MBD3 ChIP-seq experiment was perform using human breast cancer cells, MDA-MB-231. Two bilogical replicates were prepared.

ORGANISM(S): Homo sapiens

SUBMITTER: Takashi Shimbo

PROVIDER: E-GEOD-76116 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

MBD3 localization by ChIP-seq

Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression. Identification of MBD3 localization in human breast cancer cell lines

2013-10-31 | E-GEOD-44737 | biostudies-arrayexpress

ChIP-seq analysis of MBD3 in human breast cancer cells

Project description:Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful approach to identify the genome-wide localization of protein of interest. However, to perform ChIP-seq experiments for large protein complex, such as Mi-2/NuRD complex, is still challenging. Here, we present high-quality MBD3 ChIP-seq data in human breast cancer cells, MDA-MB-231.

2015-12-21 | GSE76116 | GEO

Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes [ChIP-seq]

Project description:The molecular signature at histone H3K4 involved in epigenetic regulation of normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology. This study examines the dynamic distribution of H3K4me3 and H3K4ac histone modification associated with active chromatin to provide an understanding of the changes in epigenetic regulation associated with the unique breast cancer subtypes. H3K4me3 and H3K4ac histone modification study in normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology

2016-02-10 | E-GEOD-69377 | biostudies-arrayexpress

DamID for MBD3 in human breast cancer cell lines [Promoter_Arrays]

Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression. DamID experiment was performed in human breast cancer cell lines (MCF-7 and MDA-MB-231) in duplicate. Samples were hybridized to Nimblegen 2.1M Deluxe promoter array. MBD3-Dam material was hybridized over Dam-only control.

2013-10-31 | E-GEOD-44773 | biostudies-arrayexpress

DamID for MBD3 in human breast cancer cell lines [Tiling Arrays]

Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression. DamID experiment was performed in human breast cancer cell lines (MCF-7 and MDA-MB-231) in triplicate. Samples were hybridized to NimbleGen Human Whole-Genome Tiling Arrays (0701_HG18_TILE_05_HX1 and 100718_HG18_TILE_05_HX1). MBD3-Dam material was hybridized over Dam-only control.

2013-10-31 | E-GEOD-44774 | biostudies-arrayexpress

Chromatin accessibility of a model of CRISPR-mediated insulator disruption in the MMP locus in triple-negative breast cancer cell lines

Project description:Using CRISPR-Cas9 technology, we stably disrupted an insulator element in two different TNBC cell lines. The aim of this experiment was to characterize the chromatin accessibility profile using ATAC-seq. For this experiment, we selected three biological replicates of MDA-MB-231 (WT and IE8dis) and MDA-MB-436 (WT and IE8dis).

2023-08-31 | E-MTAB-12821 | biostudies-arrayexpress

Identification of p63 binding regions in a p63 expressing basal-subtype breast cancer cell line, MCFDCIS.

Project description:p63 ChIP-SEQ in a p63 expressing basal-subtype breast cancer cell line, MCFDCIS and in a p63 deficient claudin-low subtype breast cancer cell line, MDA-MB-231 p63 ChIP-SEQ on MCFDCIS and MDA-MB-231 cell lines

2016-08-11 | E-GEOD-72009 | biostudies-arrayexpress

Identification of enhancer landscape in MDA-MB-231 cells

Project description:To identify typical enhancers and super-enhancers in the MDA-MB-231 triple-negative breast cancer cell line, we performed ChIP-seq using DNA isolated from untreated MDA-MB-231 cells using an H3K27ac antibody.

2020-02-21 | GSE95222 | GEO

ChIP-seq for ZEB1 in the human breast cancer cell line MDA-MB-231

Project description:Identification of DNA binding sites of the transcription factor ZEB1 in the human breast cancer cell line MDA-MB-231 by chromatin-immunoprecipitation followed by sequencing (ChIP-seq).

2020-07-22 | E-MTAB-8258 | biostudies-arrayexpress

ATAC-seq in control compared to ZEB1 knock-down MDA-MB-231 cells

Project description:Identification of open chromatin regions in wildtpye, control knock-down (shCtrl) and ZEB1 knock-down (shZEB1) human breast cancer MDA-MB-231 cells by ATAC(Assay for transposable-accessible chromatin)-seq.

2020-07-22 | E-MTAB-8264 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data