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Effect of DBC1/CCAR2 knockout on global gene expression in SW480 cells

ABSTRACT: Deleted in breast cancer (DBC1; also known as CCAR2) is a coactivator for nuclear receptors (NRs) and other transcription factors as well as a negative regulator of epigenetic modifiers such as deacetylases SIRT1 and HDAC3. We performed genome-wide gene expression analysis in wild-type and DBC1 knockout SW480 cells to investigate global gene expression changes induced by DBC1 knockout.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65841 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA275192

REPOSITORIES: GEO

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Effect of DBC1/CCAR2 knockout on global gene expression in SW480 cells

Project description:Deleted in breast cancer (DBC1; also known as CCAR2) is a coactivator for nuclear receptors (NRs) and other transcription factors as well as a negative regulator of epigenetic modifiers such as deacetylases SIRT1 and HDAC3. We performed genome-wide gene expression analysis in wild-type and DBC1 knockout SW480 cells to investigate global gene expression changes induced by DBC1 knockout. Total RNAs were isolated from SW480 wild-type and DBC1 knockout cells using the RNeasy mini kit (Qiagen). The integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer. Three independent biological replicates were assayed for each sample. The microarrays were performed following the Affymetrix standard protocol.

2015-12-31 | E-GEOD-65841 | biostudies-arrayexpress

Effect of DBC1/CCAR2 depletion on global gene expression in MDA-MB-231 cells

2015-01-31 | GSE54707 | GEO

Effect of DBC1/CCAR2 depletion on global gene expression in MDA-MB-231 cells

Project description:Deleted in breast cancer (DBC1; also known as CCAR2) is a coactivator for nuclear receptors (NRs) as well as a negative regulator of epigenetic modifiers such as deacetylases SIRT1 and HDAC3. We performed genome-wide gene expression analysis in control (shNS) and DBC1-depleted (shDBC1) MDA-MD-231 cells to investigate global gene expression changes induced by depletion of DBC1 Total RNAs were isolated from MDA-MB-231 cells expressing shNS or shDBC1 using the RNeasy mini kit (Qiagen). The integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer. Two independent biological replicates were assayed for each sample. The microarrays were performed following the Affymetrix standard protocol.

2015-01-31 | E-GEOD-54707 | biostudies-arrayexpress

DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [RNA-seq]

Project description:We identified DBC1/CCAR2 target genes using RNA-seq analysis in colon cancer cells.

2022-08-17 | GSE179462 | GEO

DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [HCT116 RNA-seq]

Project description:We identified DBC1/CCAR2 target genes using RNA-seq analysis in colon cancer cells.

2022-08-17 | GSE201363 | GEO

DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300.

Project description:Genome-wide maps of DBC1, KMT2D, and p300 in SW480 WT and DBC1 KO cells

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DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [ChIP-Seq]

Project description:Genome-wide maps of H3K4me3, H3K4me1, H3K27ac, H3K9/K14ac, and H3K4ac in SW480 WT and DBC1 KO cells

2022-08-17 | GSE179461 | GEO

Proteomic profile of deleted in breast cancer 1 protein-protein interactions

Project description:Deleted in breast cancer 1 (DBC1) has emerged as an important regulator of multiple cellular processes, ranging from gene expression to cell cycle progression. DBC1 has been linked to tumorigenesis both as an inhibitor of histone deacetylases (HDAC), HDAC3 and sirtuin 1 (SIRT1), and as a transcriptional cofactor for nuclear hormone receptors. However, despite mounting interest in DBC1, relatively little is known about the range of its interacting partners and the scope of its functions. DBC1 protien interactions were studied in two cell types, T cells and HEK293 kidney cells

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Human SW480 cells: Untreated vs H2O2 Treated

Project description:ChIP-on-chip tilling array comparing untreated human SW480 cells vs SW480 cells treated with 2mM H2O2 for 30min. Exposing cells to the reactive oxygen species, hydrogen peroxide, recruits DNA methyltransferase 1 (DNMT1) to damaged chromatin. DNMT1 becomes part of a complex(es) containing DNMT3B and members of Polycomb Repressive Complex 4. The goal was to determine the effect of hydrogen peroxide treatment on chromatin, including changes in histone modifications and binding patterns of chromatin-associated proteins. [Agilent-014706]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2. [Agilent-014707]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2. [Agilent-026595]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and H3. [Agilent-027811]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Four-mark: H3, 3MeK4H3, AcK16H4, and 3MeK27H3.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CCAR2-/- MDA-MB-231 cells Transcriptomes

Project description:CCAR2 has been characterized as a key regulator of physiological and pathophysiological activities, such as DNA damage, senescence and tumorigenesis. However, the mechanism by which the functional stability of CCAR2 is regulated has yet to be elucidated. We performed Next Generation Sequencing analysis in wild-type and CCAR2 knockout MDA-MB-231 cells to investigate global gene expression changes under normal or hypoxic condition.

2022-08-15 | GSE193133 | GEO

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