Mus musculus
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ABSTRACT:
PROVIDER: PRJNA99005 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression data from specific translational activity and cytoplasmic localization (nuclear retention) of mRNAs of primary mouse embryonic fibroblasts (MEF) early in response to serum. The goal of the study was to roughly discriminate between different levels of RNA regulation, namely mRNA de-novo transcription, mRNA stability and degradation, mRNA nuclear retention, mRNA translation as well as miRNA expression within a defined cellular system and time point and to link these levels together in order to get a more detailed analysis of the complex RNA regulation system, the ?RNA regulome?. To make the data more stringent the same microarray platform (Affymetrix GeneChip system) for all analyses except the miRNA expression profiling were used. Nuclear and cytoplasmic RNA fractions were separated in order to get more insight into potential nuclear retention of mRNAs. In addition the cytoplasmic mRNA pool was fractionated by its polyribosomal load using sucrose density gradients. Likewise the small RNA was specifically analyzed for miRNA precursor expression and mature miRNA expression. As study system the early serum response model of primary mouse embryonal fibroblast cells was used. Affymetrix GeneChip microarrays were used to detail regulatory mechanisms of mRNA translation and localization in response to serum (2h). Experiment Overall Design: The gene expression and regulation program at the RNA level early (2h) in response to serum was studied. mRNAs was isolated from serum starved and 2h serum treated MEF cells. This experiment allowed detailed regulatory mechanisms of mRNA translational activity and cytoplasmic localization (nuclear retention) of mRNAs of MEF cells in early response to serum.
2008-06-15 | E-GEOD-7363 | biostudies-arrayexpress
Project description:SILAC-based analysis of BRAF interaction partners in DT40 chicken cells and mouse embryonic fibroblasts (MEF)
2016-07-13 | PXD003256 | Pride
Project description:Human embryonic stem cells can be maintained in a basic Serum Replacement (Invitrogen) based medium that has been conditioned on mouse embryonic fibroblasts (MEFs), yielding MEF-CM. Ligands secreted into the medium by the MEFs include Activin A, TGFß1, and Gremlin. This experiment served the purpose of identifying the short-term effects of MEF-CM and its substitute UM_GTA (unconditioned medium plus Activin A, TGFb1, and Gremlin) on gene expression in human embryonic stem cells. Keywords: Media / growth factor stimulation experiment
2008-03-12 | GSE9059 | GEO
Project description:Expression data from specific translational activity and cytoplasmic localization (nuclear retention) of mRNAs of primary mouse embryonic fibroblasts (MEF) early in response to serum. The goal of the study was to roughly discriminate between different levels of RNA regulation, namely mRNA de-novo transcription, mRNA stability and degradation, mRNA nuclear retention, mRNA translation as well as miRNA expression within a defined cellular system and time point and to link these levels together in order to get a more detailed analysis of the complex RNA regulation system, the ?RNA regulome?. To make the data more stringent the same microarray platform (Affymetrix GeneChip system) for all analyses except the miRNA expression profiling were used. Nuclear and cytoplasmic RNA fractions were separated in order to get more insight into potential nuclear retention of mRNAs. In addition the cytoplasmic mRNA pool was fractionated by its polyribosomal load using sucrose density gradients. Likewise the small RNA was specifically analyzed for miRNA precursor expression and mature miRNA expression. As study system the early serum response model of primary mouse embryonal fibroblast cells was used. Affymetrix GeneChip microarrays were used to detail regulatory mechanisms of mRNA translation and localization in response to serum (2h). Keywords: treatment experiment
2007-03-27 | GSE7363 | GEO
Project description:Expression data of synchronised mouse embryonic fibroblasts (MEF) and synchronised primary human fibroblasts (NHDF)
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Project description:Validation of an in vitro model of hypoxia using a primary cell culture of mouse embryonic fibroblasts (MEF) exposed to 1% oxygen at 37 degrees celsius. Control cells were exposed to atmospheric oxygen.
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Project description:Current methods to analyze gene expression measure steady-state levels of mRNA. In order to specifically analyze mRNA transcription, a technique has been developed that can be applied in-vivo. The technique is referred with the acronym NIAC-NTR (Non Invasive Application and Capture of Newly Transcribed RNA). This method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in-vivo. The method has been applied to a model of serum response of cultured primary mouse embryonic fibroblasts. Affymetrix GeneChip microarrays were used to detail regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level. Experiment Overall Design: The gene expression and regulation program at the RNA level early (2h) in response to serum was studied. Total RNA, amplified total RNA and specifically enriched newly transcribed RNA was isolated from serum starved and 2h serum treated MEF cells. This experiment allowed detailed regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level of MEF cells early in response to serum.
2008-06-15 | E-GEOD-6697 | biostudies-arrayexpress
Project description:In the present study, we report proteome data of mouse embryonic fibroblasts (MEF cells) and immortalized mouse embryonic fibroblasts which are 4-OH-TAM-inducible Gpx4−/− (Pfa1 cells). Ferroptosis in Pfa1 cells was induced with Tamoxifen (Tam) addition and three timepoints were collected: 0h, 24h and 48h. Wild-type MEF cells were also measured as an alternative control without Tam addition. Raw data for HEK293 cells are provided as an independent quality control. MEF and Pfa1 cells (both kind gift from Marcus Conrad, Munich) were cultured in RPMI-1640 media (2 g/L glucose, 10% FBS, 2 mM Gibco GlutaMAX Supplement, 1% pen/strep) at 37C with 5% CO2 in a humidified incubator. Cells (300k) were seeded on Corning 100 mm tissue-culture treated culture dishes and incubated overnight. On the next day Pfa1 cells were treated with or without 1 µM Tam.
2023-04-12 | PXD040094 | Pride
Project description:Mouse Ikbkap gene encodes IKAP/Elp1- one of the core subunits of Elongator- and has been implicated in translational regulation. However, a role for IKAP in genome maintenance remains unclear. In this study, we analyze proteins from control and Ikbkap depletion mouse embryonic fibroblasts (MEF) using MS. Using MS-based proteomics, we show that several proteins involved in cancer and DNA damage response were found to be differentially expressed upon Ikbkap depletion.
2022-02-17 | PXD024628 | Pride
Project description:Transcriptional response to stress in serum deprived mouse fibroblasts
| PRJNA239956 | ENA