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Genes regulated by SMAD3 in HCC cells

ABSTRACT: Genes regulated by SMAD3 in HCC cells

PROVIDER: PRJNA548278 | ENA |

REPOSITORIES: ENA

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Genes regulated by SMAD3 in HCC cells

Project description:To identify genes regulated by SMAD3, we have employed whole transcriptome microarray expression profiling to identify genes downstream of SMAD3. Total RNAs from SMAD3-overexpression (7721-SMAD3 vs 7721-VEC) or SMAD3-knockdown (LM3-shSMAD3 vs LM3-CON) cell lines were measured.

2022-06-10 | GSE132518 | GEO

Investigation of downstream genes regulated by ACOT12 in HCC cells

Project description:Investigation of downstream genes regulated by ACOT12 in HCC cells

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Investigation of downstream genes regulated by ACOT12 in HCC cells [Huh7]

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Investigation of downstream genes regulated by ACOT12 in HCC cells [MHCC97H]

Project description:Investigation of downstream genes regulated by ACOT12 in HCC cells [MHCC97H]

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SMAD3 and SOX4 binding profiling in human breast cell lines

Project description:In order to identify genes co-bound by SOX4 and SMAD3 in the context of breast cancer, different breast cell lines (HMLEs, MDA-MB-231 or HCC-1954) were used. Due to low endogenous expression levels for SOX4 in HMLEs in untreated conditions, doxycycline-dependent SOX4 overexpression was obtained by transducing HMLE cells with pIINDUCER21-SOX4 vector..Cells were plated and SOX4 and SMAD3 chromatine-immunoprecipitation was performed in untreated conditions, TGF-beta (2.5ng/ml), doxycycline (0.5ug/ml) or both as indicated. Genome-wide binding sites for SOX4 and SMAD3 was identified in HMLEs, MAD-MB-231 and HCC-1954 cells.

2018-06-11 | GSE104760 | GEO

Transcriptomic analysis of the RPS3-regulated genes in HCC cell line

Project description:Transcriptomic analysis of the RPS3-regulated genes in HCC cell line

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Nrf2 regulated genes in A549 cells

Project description:Nrf2 regulated genes in A549 cells

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SMAD3 targets in A549 lung epithelial cells

Project description:TGF? activates a signal transduction cascade that results in the transcription of genes, primarily through the DNA-binding transcription factor SMAD3. The objective of this study is to identify SMAD3 binding targets and the molecular pathways affected by the TGF?1/SMAD3 signal transduction on a genome-wide scale. Cultured A549 cells at 30-50% confluence were treated with 10 uM SIS3 in dimethyl sulfoxide (DMSO), or DMSO (vehicle-only) 30 min prior to TGF?1 treatment. Cells were treated with 2 ng/mL recombinant TGF?1 for 0, 2, 12, and 24 h.

2011-06-24 | E-GEOD-26858 | biostudies-arrayexpress

ChIP-seq to reveal the genomic binding landscape of Smad3 in renal tubular cells TCMK1

Project description:Smad3 is an important downstream transcriptional factor of TGF-β signaling in the pathogenesis of renal fibrosis. Understanding the target genes is essential to decode the mechanism underlying Smad3-regulated renal fibrosis. To uncover the potential target genes of Smad3 in renal tubular cells, we applied the ChIP-seq technology to analyze the genomic chromatin binding landscape of Smad3 in TCMK-1 cells. The TCMK-1 cells of 90% confluence were starved in low-serum (0.5% FBS) medium for 6 h followed by stimulation with 5 ng/ml TGF-β1 for 30 min. The cells were harvested for ChIP assay. The precipitated chromatin was used for DNA isolation and deep-sequencing.

2022-07-19 | GSE203063 | GEO

Expression data from C2C12 cells with or without Smad3 overexpression

Project description:The goal of this study was to identify genes in C2C12 myoblasts whose expression was altered by overexpression of Smad3. Four total samples were analyzed. Two biological replicates were prepared from C2C12 cells infected with retroviral vector encoding wildtype Smad3 and exposed for 24 hours to 100 pM TGF-β. Two biological replicates were prepared from C2C12 cells infected with a control retrovirus that did not encode Smad3 (empty vector, EV) and exposed for 24 hours to 100pM TGF-β. To identify genes with altered expression between empty vector controls and cells overexpressing wild-type Smad3, we first pre-processed the four arrays using robust multiarray averaging as implemented in the R software package ‘xps’, version 1.10.2 (http://www.bioconductor.org/packages/release/bioc/html/xps.html). This preprocessing corrects for background noise and array effects, and aggregates probe data to 28,836 genes. Duplicates were averaged on the base-2 logarithm scale, and then we took differences between the averages to obtain logarithm-scale fold changes. Genes were selected which showed at least a two-fold change (raw scale) between wild-type and empty vector expressing cells. Due to the limited sample size, we did not apply any statistical tests to estimate false-discovery rate. This resulted in 79 genes that were at least two-fold higher in the wild-type Smad3-expressing C2C12 cells compared to empty vector cells and 25 genes that were at least two-fold lower in the wild-type Smad3-expressing cells than the in the empty vector cells.

2011-10-20 | E-GEOD-30459 | biostudies-arrayexpress

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