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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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TGF-beta1-Induced Gene Expression Changes in HepG2 Cells

ABSTRACT: We here compared gene expression profiles in HepG2 cells upon stimulation with 1 ng/ml TGF-beta1 for 20 min, 1 hour, 2 hours, 4 hours, and 24 hours with untreated control cells. Experiments were done in three independent replicates. The goal of this study was to determine genes regulated by TGF-beta1.HepG2 cells were obtained from DSMZ (Braunschweig, Germany) and cell identity confirmed by STR profiling using the AmpFlSTR Identfiler Direct PCR Amplification kit (Life Technologies, Darmstadt, Germany). Gene expression profiles were compared at indicated time points after stimulation with TGF-beta (1 ng/ml) using the Human Gene 1.0 ST arrays (Affymetrix). In total 18 hybridizations are included in this series. 18 samples were hybridized to Affymetrix Human Gene 1.0 ST Array

ORGANISM(S): Homo sapiens

SUBMITTER: Ralf Weiskirchen

PROVIDER: E-GEOD-45945 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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TGF-beta1-Induced Gene Expression Changes in HepG2 Cells

Project description:We here compared gene expression profiles in HepG2 cells upon stimulation with 1 ng/ml TGF-beta1 for 20 min, 1 hour, 2 hours, 4 hours, and 24 hours with untreated control cells. Experiments were done in three independent replicates. The goal of this study was to determine genes regulated by TGF-beta1.HepG2 cells were obtained from DSMZ (Braunschweig, Germany) and cell identity confirmed by STR profiling using the AmpFlSTR Identfiler Direct PCR Amplification kit (Life Technologies, Darmstadt, Germany). Gene expression profiles were compared at indicated time points after stimulation with TGF-beta (1 ng/ml) using the Human Gene 1.0 ST arrays (Affymetrix). In total 18 hybridizations are included in this series.

2013-04-10 | GSE45945 | GEO

Transcription profiling of human hematopoietic stem/progenitor cells treated with TGF-beta1 to idetntify its target genes

Project description:CD34+ hematopoietic stem/progenitor cells were isolated from human cord blood and amplified in vitro for 10-14 days in serum-free medium with specific cytokines (Ju et al., Eur. J. Cell Biol. 82, 75-86, 2003; Hacker et al., Nat. Immunol. 4, 380-386, 2003). Cells were then treated with TGF-beta1 for various periods of time (2, 4, 16 hours) and RNA was prepared and subjected to microarray analysis. Experiment Overall Design: CD34+ hematopoietic stem/progenitor cells (HPC) were amplified in vitro and treated with TGF-beta1 (10 ng/ml) for 2, 4 and 16 hours. Experiment Overall Design: HPC untreated Experiment Overall Design: HPC + TGF-beta1 for 2 hours Experiment Overall Design: HPC + TGF-beta1 for 4 hours Experiment Overall Design: HPC + TGF-beta1 for 16 hours

2008-06-13 | E-GEOD-5150 | biostudies-arrayexpress

Dynamic Gene Expression Response to TGF-b Stimulation in Multipotent Progenitors and Common Dendritic Cell Progenitors

Project description:Multipotent progenitors (MPP) and common dendritic cell progenitors (CDP) were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Sere et al., 2012). Cells were treated with 10 ng/ml recombinant human TGF-b1 (R&D Systems, Minneapolis, USA) for 2, 4, 8, 12 and 24 h as described (Felker et al., 2010) or left untreated. Untreated multipotent progenitor (MPP) - MPP_0h_1 - MPP_0h_2 - MPP_0h_3 TGF-beta1 treated (2 hours) MPP - MPP_2h_1 - MPP_2h_2 - MPP_2h_3 TGF-beta1 treated (4 hours) MPP - MPP_4h_1 - MPP_4h_2 - MPP_4h_3 TGF-beta1 treated (8 hours) MPP - MPP_8h_1 - MPP_8h_2 - MPP_8h_3 TGF-beta1 treated (12 hours) MPP - MPP_12h_1 - MPP_12h_2 - MPP_12h_3 TGF-beta1 treated (24 hours) MPP - MPP_24h_1 - MPP_24h_2 - MPP_24h_3 Untreated common dendritic cell progenitor (CDP) - CDP_0h_1 - CDP_0h_2 - CDP_0h_3 TGF-beta1 treated (2 hours) CDP - CDP_2h_1 - CDP_2h_2 - CDP_2h_3 TGF-beta1 treated (4 hours) CDP - CDP_4h_1 - CDP_4h_2 - CDP_4h_3 TGF-beta1 treated (8 hours) CDP - CDP_8h_1 - CDP_8h_2 - CDP_8h_3 TGF-beta1 treated (12 hours) CDP - CDP_12h_1 - CDP_12h_2 - CDP_12h_3 TGF-beta1 treated (24 hours) CDP - CDP_24h_1 - CDP_24h_2 - CDP_24h_3

2014-04-15 | E-GEOD-46109 | biostudies-arrayexpress

Transcription profiling of human cord blood derived CD34+ hematopoietic stem/progenitor cells to identifyTGF-beta1 target genes in human dendritic cells (DC).

Project description:CD34+ hematopoietic stem/progenitor cells were isolated from human cord blood and amplified in vitro for 10-14 days in serum-free medium with specific cytokines (Ju et al., Eur. J. Cell Biol. 82, 75-86, 2003; Hacker et al., Nat. Immunol. 4, 380-386, 2003). Cultured progenitor cells were induced to differentiate into DC in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 microM Beta-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO-BRL) and 500 U/ml GM-CSF, 500 U/ml IL-4 for 6 days with or without 10 ng/ml TGF-beta1 as indicated (0.5x10E6 cells/ml). Every 2 days growth factors were added and cells were maintained at 0.5x10E6 cells/ml cell density. RNA was prepared and subjected to microarray analysis. Experiment Overall Design: Dendritic cells (DC) were treated for various periods of time (4, 16 and 36 hours) with TGF-beta1 (10 ng/ml) or left untreated. Experiment Overall Design: DC untreated Experiment Overall Design: DC + TGF-beta1 for 4 hours Experiment Overall Design: DC + TGF-beta1 for 16 hours Experiment Overall Design: DC + TGF-beta1 for 36 hours

2008-06-13 | E-GEOD-5151 | biostudies-arrayexpress

TGF-beta1-Induced Gene Expression Changes in Primary Murine Hepatocytes

Project description:We here compared gene expression profiles of primary murine hepatocytes (mPC) upon stimulation with 1 ng/ml TGF-beta1 for 20 min, 2 hours and 4 hours with untreated cells. Experiments were done in three independent replicates. The goal of this study was to determine genes regulated by TGF-beta1. 12 samples were hybridized to Affymetrix Mouse Gene 1.0 ST Array

2013-04-10 | E-GEOD-45942 | biostudies-arrayexpress

TGF-beta1-Induced Gene Expression Changes in Primary Murine Hepatocytes

2013-04-10 | GSE45942 | GEO

Transcription profiling of human hematopoietic stem/progenitor cells and dendritic cells to identify TGF-beta1 target genes

Project description:This SuperSeries is composed of the following subset Series:; GSE5150: TGF-beta1 target genes in human hematopoietic stem/progenitor cells. GSE5151: TGF-beta1 target genes in human dendritic cells (DC). Experiment Overall Design: Refer to individual Series

2008-11-06 | E-GEOD-5178 | biostudies-arrayexpress

Transcription profiling of human tongue carcinoma cells treated with emdogain and TGF beta1

Project description:Background: The composition of Emdogain® (EMD) is unclear, but it has been postulated to contain transforming growth factor-beta-1 (TGF-beta1) as the main functioning cytokine. The purpose of this study was to compare target genes of EMD and TGF-beta1 on invasive oral carcinoma HSC-3 cells. Particular focus was on matrix metalloproteinase (MMP) family genes. <br>Methodology/Principal Findings: Affymetrix microarrays were conducted to study differentially (P<0.05) expressed genes in HSC-3 cells after 6h and 24h of EMD (200 ?g/ml) or TGF-beta1 (10 ng/ml) incubations. Gene Ontology (GO) enrichment analyses from the regulated genes were also conducted. After 6h of EMD or TGF-?1 treatment, 48 and 393 genes, respectively, were regulated. After 24h incubations, only 12 genes by EMD but 346 genes by TGF-beta1 were regulated. Among the most regulated genes by both of the study reagents were several genes commonly regulated in carcinomas, including MMP-9 and -10. The expression of MMP-10 by EMD treated carcinoma cells was also verified in protein level. <br>Conclusions/Significance: Our results show that EMD and TGF-beta1 can regulate genes related to carcinogenesis, but TGF-beta1 regulates significantly greater number of genes. This suggests that TGF-beta1 cannot be present in EMD at the studied concentration, if present at all.<br>

2010-04-30 | E-MEXP-2645 | biostudies-arrayexpress

TGF-beta and BMP mediated gene expression in cultured sclerotome.

Project description:Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-beta superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-beta has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-beta action in these specialized joints is not known. To understand the mechanism of TGF-beta action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in sclerotome cultures treated with TGF-beta or BMP4. As expected, treatment with BMP4 resulted in up-regulation of cartilage marker genes including Acan, Sox 5, Sox6, and Sox9. In contrast, treatment with TGF-beta1 did not regulate expression of cartilage markers but instead resulted in up-regulation of many IVD markers including Fmod and Adamtsl2. We propose TGF-beta has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-beta that warrant further investigation as regulators of IVD development. Nine samples were analyzed. Three biological replicates of untreated sclerotome grown in micromass culture. Three biological replicates of cells treated with 50 ng/ml BMP4 for 8 hours and three biological replicates of cells treated with 5 ng/ ml TGF-beta1 for 8 hours.

2010-04-09 | E-GEOD-18648 | biostudies-arrayexpress

A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (Th17 Treg)

Project description:In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS. We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS. NaÃ¯ve CD4+ T cells were isolated from buffy coat of four healthy donors using a naÃ¯ve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). NaÃ¯ve CD4+ T cells were stimulated with TGF-Î² (1 ng/mL), IL-1Î² (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-Î² (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscoveâs modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 ÂµM Î²âmercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufactureâs instruction (Agilent Technologies).

2015-11-12 | E-GEOD-60679 | biostudies-arrayexpress

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