MiRNA profiling during adipogenic differentiation of adipose-derived stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Kevin Lebrigand
PROVIDER: E-GEOD-25715 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Analysis of human adipose tissue-derived stem cells (hMADS cells) overexpressing either miR-30a or miR-30d, as well as knocked-down for the whole miR-30 family. Gene expression was analyzed after 4 days in adipogenic medium. Data give insight into the role of miR-30 during adipogenesis, and identifies enriched predicted targets for miR-30. Human adipose tissue-derived stem cells (hMADS cells) were transfected with one of the following: premiR-30a (Ambion), premiR-30d (Ambion), premiR negative control #1 (Ambion). Three days after transfection, cells were submitted to adipogenic differentiation for 4 days. In a separate experiment, hMADS cells were transfected with either antimiR-30 or antimiR-neg (mismatch control), and then submitted to differentiation as described above. For each experimental condition, 2 hMADS cell clones were used independently (clone B7 and B9).
2011-07-03 | E-GEOD-29207 | biostudies-arrayexpress
Project description:Post-transcriptional regulation of gene expression accomplished by microRNAs (miRNAs) importantly affects the complex gene regulatory network. In particular, miRNAs are known to be involved in recurrent motifs named miRNA-mediated feed forward loops (FFLs) where a transcription factor (TF) regulates a miRNA and they both regulate the expression level of a target RNA. Here, we focus on the identification of active FFLs during adipogenic differentiation. A list of putative feed-forward loops was generated based on sequence analysis of conserved and overrepresented motifs in the regulatory regions. Since this approach is not specific for adipogenesis and is known to generate false positive feed-forward loops, an experiment was designed to select active ones based on their dynamics using a model-based approach. Microarray time series of gene and miRNA expression data were collected at seven time points on human multipotent adipose-derived stem (hMADS) cells upon adipogenic differentiation. Three different dynamic models, sharing the same FFL topology but incorporating descriptions of increasing complexity of miRNA and mRNA dynamics, are identified on miRNA and mRNA expression data and compared based on identification criteria, namely: goodness of fit, precision of the estimates and comparison with submodels. 24 FFLs, able to properly reproduce data, are selected as active out of the 329 putative ones. This method considerably reduces the search space for new interactions between TFs, miRNAs and mRNAs and provides interesting biological results identifying genes known from the literature to be regulators in adipogenesis and adipocyte-related functions that can be interpreted as positive control of the validity of the apporoach. Therefore, the genes in the selected FFLs that are not yet known to be involved in this context are potential novel players in this regulatory network of adipogenesis and adipocyte function. Two independent cell culture experiments were performed as biological replicates during adipogenic differentiation of human mesenchymal stem cell. Cells where harvested at the pre-confluent stage as reference (day -3) and at seven subsequent time points during human adipogenic differentiation: day -2 and 0 before, and 1, 2, 5, 10, 15 days after induction of differentiation. All hybridizations were repeated with reversed dye assignment (dye-swap).
2011-12-20 | E-GEOD-29185 | biostudies-arrayexpress
Project description:Post-transcriptional regulation of gene expression accomplished by microRNAs (miRNAs) importantly affects the complex gene regulatory network. In particular, miRNAs are known to be involved in recurrent motifs named miRNA-mediated feed forward loops (FFLs) where a transcription factor (TF) regulates a miRNA and they both regulate the expression level of a target RNA. Here, we focus on the identification of active FFLs during adipogenic differentiation. A list of putative feed-forward loops was generated based on sequence analysis of conserved and overrepresented motifs in the regulatory regions. Since this approach is not specific for adipogenesis and is known to generate false positive feed-forward loops, an experiment was designed to select active ones based on their dynamics using a model-based approach. Microarray time series of gene and miRNA expression data were collected at seven time points on human multipotent adipose-derived stem (hMADS) cells upon adipogenic differentiation. Three different dynamic models, sharing the same FFL topology but incorporating descriptions of increasing complexity of miRNA and mRNA dynamics, are identified on miRNA and mRNA expression data and compared based on identification criteria, namely: goodness of fit, precision of the estimates and comparison with submodels. 24 FFLs, able to properly reproduce data, are selected as active out of the 329 putative ones. This method considerably reduces the search space for new interactions between TFs, miRNAs and mRNAs and provides interesting biological results identifying genes known from the literature to be regulators in adipogenesis and adipocyte-related functions that can be interpreted as positive control of the validity of the apporoach. Therefore, the genes in the selected FFLs that are not yet known to be involved in this context are potential novel players in this regulatory network of adipogenesis and adipocyte function. Two independent cell culture experiments were performed as biological replicates during adipogenic differentiation of human mesenchymal stem cell. Cells where harvested at the pre-confluent stage as reference (day -3) and at seven subsequent time points during human adipogenic differentiation: day -2 and 0 before, and 1, 2, 5, 10, 15 days after induction of differentiation. All hybridizations were repeated with reversed dye assignment (dye-swap).
2011-12-20 | E-GEOD-29182 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29182: Identification of active microRNA/transcription factor feed-forward loops during human adipogenesis (mRNA) GSE29185: Identification of active microRNA/transcription factor feed-forward loops during human adipogenesis (miRNA) Refer to individual Series
2011-12-20 | E-GEOD-29186 | biostudies-arrayexpress
Project description:Genome-wide profiling of PPAR?:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis. Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activated receptor gamma (PPARg) and retinoid X receptor (RXR) binding sites, and RNA polymerase II (RNAPII) occupancy at high resolution throughout adipocyte differentiation of 3T3-L1 cells. The data provides the first positional and temporal map PPAR? and RXR occupancy during adipocyte differentiation at a global scale. The number of PPAR?:RXR shared binding sites is steadily increasing from D0 to D6. At Day6 there are over 5000 high confidence shared PPARy:RXR binding sites. We show that at the early days of differentiation several of these sites bind not only PPAR?:RXR but also other RXR dimers. The data also provides a comprehensive temporal map of RNAPII occupancy at genes throughout 3T3-L1 adipogenesis thereby uncovering groups of similarly regulated genes belonging to glucose and lipid metabolic pathways. The majority of the upregulated but very few downregulated genes have assigned PPAR?:RXR target sites, thereby underscoring the importance of PPAR?:RXR in gene activation during adipogenesis and indicating that a hitherto unrecognized high number of adipocyte genes are directly activated by PPAR?:RXR Examination of PPARg and RXR bindingsites during adipocyte differentiation (day 0 to 6) and association with transcription via RNAPII occupancy.
2008-12-10 | E-GEOD-13511 | biostudies-arrayexpress
Project description:Transcriptional profiling of hMADS cells treated or not by TCDD, PCB126 and PCB153. Four-condition experiment: 4 control replicates, 4 TCDD-treated, 4 PCB126-treated, 4 PCB153-treated either undiffrentitaed or differentiated cells.
2011-09-09 | E-GEOD-32026 | biostudies-arrayexpress
Project description:3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media. Two technical replicates from four time points relative to induction of adipogenesis (day 0)
2010-09-30 | E-GEOD-20696 | biostudies-arrayexpress
Project description:miRNA profiles of adipocyte-derived microvesicles (ADMs) on the Day 2-4 and Day 8-10 were compared. ADMs were prepared from the 48h-conditioned medium of 3T3-L1 adipocytes (Day 2-4 and Day 8-10) followed by RNA isolation.
2010-07-06 | E-GEOD-17977 | biostudies-arrayexpress
Project description:We report that terahertz (THz) irradiation of mouse mesenchymal stem cells with a pulsed broadband (centered at 10 THz) source, or a single-frequency, 2.52 THz, (SF) laser source, both with weak average power (<1mW/cm2), results in specific heterogenic changes in gene expression. The insignificant differential expression of heat shock and stress related genes as well as our temperature measurements imply a non-thermal response. The microarray survey and RT-PCR experiments demonstrate that at different irradiation conditions distinct groups of genes are activated. Stem cells irradiated for 12 hours with the broadband THz source exhibit an accelerated differentiation toward adipose phenotype, while the 2-hour (broadband or SF) irradiation affects genes transcriptionally active in pluripotent stem cells. Phenotypic and gene expression differences suggest that the THz effect depends on irradiation parameters such as duration and type of THz source, and on the level of stem cell differentiation. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression. Growing in petri dish mouse mesenchymal stem cell cultures are irradiated for 12 hours with pulsed ultrafast (35 fs) broadband (centered at ~10 THz) source. Three independent biological experiments were conducted. In each experiment, a control mMSC culture was placed adjacent to the irradiated sample, and the temperature was kept at 26-27M-BM-:C for both the control and the irradiated sample. Immediately after completing the irradiation, total RNA was extracted from the irradiated sample and the control, and microarrays were used to identify differential changes in gene expression between the irradiated sample and its respective control. In each experiment, the mMSC cultures were synchronized to be at the same differentiation time point immediately before the irradiation.
2013-07-01 | E-GEOD-41084 | biostudies-arrayexpress
Project description:We report that terahertz (THz) irradiation of mouse mesenchymal stem cells with a pulsed broadband (centered at 10 THz) source, or a single-frequency, 2.52 THz, (SF) laser source, both with weak average power (<1mW/cm2), results in specific heterogenic changes in gene expression. The insignificant differential expression of heat shock and stress related genes as well as our temperature measurements imply a non-thermal response. The microarray survey and RT-PCR experiments demonstrate that at different irradiation conditions distinct groups of genes are activated. Stem cells irradiated for 12 hours with the broadband THz source exhibit an accelerated differentiation toward adipose phenotype, while the 2-hour (broadband or SF) irradiation affects genes transcriptionally active in pluripotent stem cells. Phenotypic and gene expression differences suggest that the THz effect depends on irradiation parameters such as duration and type of THz source, and on the level of stem cell differentiation. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression. Growing in petri dish mouse mesenchymal stem cell cultures are irradiated for 2 hours with pulsed ultrafast (35 fs) broadband (centered at ~10 THz) source. Three independent biological experiments were conducted. In each experiment, a control mMSC culture was placed adjacent to the irradiated sample, and the temperature was kept at 26-27M-BM-:C for both the control and the irradiated sample. Immediately after completing the irradiation, total RNA was extracted from the irradiated sample and the control, and microarrays were used to identify differential changes in gene expression between the irradiated sample and its respective control. In each experiment, the mMSC cultures were synchronized to be at the same differentiation time point immediately before the irradiation.
2013-07-01 | E-GEOD-41083 | biostudies-arrayexpress