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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MEF wt versus Med23-/- KO after 20% Serum Stimulation

ABSTRACT: Affymetrix MOE430A arrays. Mouse embryonic fibroblasts (MEFs) from E11 passaged through crisis. Starved in 0.5% FBS for 16 h then stimulated by 20% serum final concentration for 30 minutes. The purpose was to identify genes affected by the loss of MED23 protein (subunit of the mediator complex). Samples were assayed in duplicate (Set 1 and Set 2) for starved state and serum state cells. Cells starved in low-serum (0.5%) for 16 h then add final conc. 20% FBS for 30 minutes. Harvest total RNA from duplicate samples. One sample set is kept starved and serves as the baseline. The other set is stimulated. This is done for both wild-type cell and the Med23-/- KO cells. We looked for gene expression fold changes greater than 2 (plus or minus) to find genes affected for serum stimulation by the loss of MED23, looking in detail at immediate early genes like Egr1.

ORGANISM(S): Mus musculus

SUBMITTER: Michael Balamotis

PROVIDER: E-GEOD-15638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Complexity in transcription control at the activation domain-mediator interface.

Balamotis Michael A MA Pennella Mario A MA Stevens Jennitte L JL Wasylyk Bohdan B Belmont Andrew S AS Berk Arnold J AJ

Science signaling 20090505 69

Transcript elongation by polymerase II paused at the Egr1 promoter is activated by mitogen-activated protein kinase phosphorylation of the ternary complex factor (TCF) ELK1 bound at multiple upstream sites and subsequent phospho-ELK1 interaction with mediator through the MED23 subunit. Consequently, Med23 knockout (KO) nearly eliminates Egr1 (early growth response factor 1) transcription in embryonic stem (ES) cells, leaving a paused polymerase at the promoter. Med23 KO did not, however, elimina ...[more]

PMID: 19417216

Similar Datasets

MEF wt versus Med23-/- KO after 20% Serum Stimulation

Project description:Affymetrix MOE430A arrays. Mouse embryonic fibroblasts (MEFs) from E11 passaged through crisis. Starved in 0.5% FBS for 16 h then stimulated by 20% serum final concentration for 30 minutes. The purpose was to identify genes affected by the loss of MED23 protein (subunit of the mediator complex). Samples were assayed in duplicate (Set 1 and Set 2) for starved state and serum state cells.

2009-04-14 | GSE15638 | GEO

Genome-wide analysis of serum starved prelamin A-accumulating hMSCs gene expression.

Project description:Analysis of serum starved prelamin A-accumulating hMSCs at gene expression level. The hypothesis tested in the present study was that prelamin A accumulation induces the dysregulation of genes that are essensial for cell survival under a stress condition such as serum starvation. The results provide important information about these genes and the functional categories that are dysregulated due to prelamin A accumulation in serum starved hMSCs. Two samples are analyzed in this microarray experiment: human mesenchymal stem cell cultured under serum starvation conditions (during 24 hours) which accumulate prelamin A (pre-hMSCs) and control mesenchymal stem cells (ctrl-hMSCs). 2 biological replicates (hMSCs derived from 2 different bone marrow donors) and 1 technical replicate are included in this analysis.

2014-06-23 | E-GEOD-52563 | biostudies-arrayexpress

Identify the downstream targets of Stat3 by using an engineered mouse ES cell line treated with GCSF and LIF plus PD0325901

Project description:To identify downstream targets of Jak/Stat3 pathways without being distracted by differentiation signalings from MEK/ERK pathway, we exploited a engineered B6 cells, which stably stably expressing a chimeric receptor (GRgp-Y118F). The chimeric receptor can induce the phosphorylation of Stat3 by GCSF without activating the MEK/ERK pathway. To mimic the effect of GCSF, the chimeric B6 cells were also treated with LIF plus a selective MEK chemical inhibitor, PD0325901, to induce LIF/Jak/Stat3 but MEK/ERK pathways. mESCs starved in serum free growth medium for 6hrs were treated with GCSF or with LIF plus PD0325901 for 1hr, after which total RNA was extracted for analysis.

2012-06-13 | E-GEOD-38719 | biostudies-arrayexpress

Transcription profiling of SrcR388A/Y527F or SrcD386N/Y527F stably transfected SYF cells serum-starved overnight and then treated with imidazole 5 mM for 1 h or 12 reveals that the protein tyrosine kinase Src R388A mutant can be rescued in live cells using the small molecule imidazole

Project description:SrcR388A/Y527F or SrcD386N/Y527F stably transfected SYF cells were serum-starved overnight and then treated with imidazole 5 mM for 1 h or 12 h. RNeasy Miniprep column (Qiagen) was used to prepare total RNA from each treatment group. All samples were run in commercial arrays from Affymetrix,

2007-12-12 | E-GEOD-4043 | biostudies-arrayexpress

miRNA expression profile in MDA-MB-231 cells on LPA stimulation

Project description:LPA is a natural bioactive lipid with growth factor-like functions due to activation of series of six G protein-coupled receptors (LPA1-6). In this study we determine the LPA induced early-miRNA expression profile in human breast cancer cell lines MDA-MB-231 MDA-MB-231 cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min. The controls were the serum starved unstimulated cells. Three replicates were included in this study.

2015-05-05 | E-GEOD-64100 | biostudies-arrayexpress

The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

Project description:We examined how MED23 regulates SRF-targeted genes by comparing WT and Med23 KO mouse embryonic fibroblasts (MEFs) in the presence or absence of serum-stimulation (for 30 and 90 min). To investigate whether MAL antagonizes MED23 in the adipocyte lineage program, we compared the gene expression changes resulting from Mal overexpression (oxMal) and Med23 deficiency (siMed23) in 10T1/2 cell. In MEF cells, we examined SRF-dependent gene expression in three time points (0, 30, 90min) and two conditions (WT and KO). In 10T1/2 cells, we used three treatment conditions (Mal overexpression, Med23 knockdown, and treatment of both Mal overexpression and Med23 knockdown) with control (no treatment).

2012-10-01 | E-GEOD-40286 | biostudies-arrayexpress

TGF-beta responsive gene in primary osteoblast.

Project description:Gene expression profiling of a total of 3,774 genes in primary osteoblastic cells treated with TGF-beta1 Keywords: cytokine response Primary osteoblasts cultured under serum-starved condition were treated or untreated with TGF-beta1 for 24 hr.

2009-04-28 | E-GEOD-11702 | biostudies-arrayexpress

Gene expression profile of LAPC4 stimulated by 5Î±-Abi

Project description:LAPC4 cells were starved for 2 days and stimulated with 1ÂµM 5Î±-Abi or 0.1nM DHT. Gene expression profiles are detected to determine the effect of 5a-Abi on prostate cancer cell line. LAPC4 cells were starved for 2 days with phenol red-free and serum free-medium and stimulated with 1ÂµM 5Î±-Abi or 0.1nM DHT for 48h. Gene expression profiles are detected to determine the effect of 5a-Abi on prostate cancer cell line.

2016-03-01 | E-GEOD-75387 | biostudies-arrayexpress

Screening of genes activated by phsiological E2F induced by gorwth stimulation

Project description:To identify genes activated by physiological E2F, we examined gene expression profiles using human normal fibroblasts (HFFs), which were starved of serum and re-stimulated with serum. To identify genes activated by growth stimulation, human normal fibroblasts (HFFs) were starved of serum for 48 hr, re-stimulated with serum or left serum-starved for 18 hr, and harvested. Gene expression profiles of each sample were examined by DNA microarray.

2015-11-20 | E-GEOD-68081 | biostudies-arrayexpress

Rapamycin effect on Wild Type and TSC deficient Mouse Embryonic Fibroblasts : Time Course

Project description:Aberrant activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a common molecular event in a large variety of pathological settings, including genetic tumor syndromes, cancer, and obesity. However, the cell intrinsic consequences of mTORC1 activation remain poorly defined. Here, we identify global trancriptional changes in TSC1 and TSC2 null MEFs, which exhibit constitutive activation of mTORC1, compared to wild-type littermate control lines. A rapamycin time course is included to determine those changes that are dependent on mTORC1 signaling, revealing mTORC1 induced and repressed transcripts. In order to identify mTORC1-dependent transcriptional changes, we compared wild-type MEFs to both Tsc1-/- and Tsc2-/- MEFs following serum starvation, where mTORC1 signaling is off in wild-type cells and fully active in TSC-deficient cells. All cell lines were serum-starved for 24 h, and the Tsc1-/- and Tsc2-/- cells were treated with a time course of rapamycin prior to the isolation of mRNA for microarray analysis. Immortalized wild-type (Tsc2+/+ p53-/-), Tsc1-/- (p53+/+, 3T3-immortalized), and Tsc2-/- (p53-/-, derived from a littermate of the wild-type cell line) MEFs are the three cell lines used in this study and were derived in the laboratory of David J. Kwiatkowski (Brigham and Women's Hospital, Harvard Medical School, Boston, MA). Wild-type and null MEFs were grown to 70% confluence in 10 cm plates and were serum starved for 24 h in the presence of vehicle (DMSO) for 24 h or rapamycin (20 nM) for 2, 6, 12, or 24 h. All vehicle-treated samples (0 h time points) were plated in triplicate and all rapamycin time course samples were plated in duplicate. For each replicate, expression analysis was performed by hybridization to an Affymetrix Mouse 430_2 oligonucleotide microarray chip.

2010-07-30 | E-GEOD-21755 | biostudies-arrayexpress

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