Project description:XAB2 ChIP-Seq profile of mESCs treated with trans-retinoic acid (tRA), a pleiotropic factor known to activate transcription and regulate gene expression during cell differentiation and embryonic development and CHIP-Seq profile of the same cells untreated.
Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles time-resolved transcriptional changes in response to NuRD induction.
Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset maps time-resolved DNA association of NuRD complex members, pluripotency factors, components of the RNA polymerase II machinery and changes to histone modifications.
Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles nascent RNA transcription in response to NuRD induction.
Project description:Nanog null neural stem (NS) cells were reprogrammed to naive pluripotency in 2i/LIF conditions with chick (c) and zebrafish (z) Nanog orthologs. Global gene expression was compared to iPS cells derived with mouse (m) Nanog. Murine iPS cells derived with zebrafish nanog, chick nanog, and mouse nanog orthologs (2 replicates each).
Project description:Nanog null neural stem (NS) cells were reprogrammed to naive pluripotency in 2i/LIF conditions with mouse (m) Nanog and human (h) Nanog. Global gene expression in resulting iPS cells was compared to embryonic stem (ES) cells and nanog null NS cells. Murine iPS cells derived with mouse nanog iPS and human nanog iPS and then compared to embryonic stem cells and nanog null neural stem cells (3 replicates each).
Project description:We have generated iPS cell lines with constitutive Oct4 expression at ES-cell level or 3 times lower. The aim of the experiment was to compare the global gene expression profile between these two cell lines and also between each of them and wild type ES cells. We have analysed two biological replicates of each cell line
Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 4 naive ES samples in 4i/LA, 3 naive ES samples in 5i/LA, 2 transgene-dependant naive ES cell samples, and 5 primed ES cell samples (in hESM)
Project description:SW480R is an APC mut, KRAS mut, P53 mut CRC cell line. PROX1 transcription factor, target of Wnt pathway in CRC, is our protein of interest.SW480R cells are PROX1 positive. We suppressed through siRNA transfection the expression of PROX1 protein or non-targeting siRNA, using two different siRNA. Afterwards we compared the transcriptional program of the SW480-PROX1si and SW480R-CTRsi cells growing in monolayer in vitro.
Project description:To get insight in the functional role of EGR2 for Ewing sarcoma, we performed a transcriptional profiling of Ewing sarcoma cells after knockdown of EGR2 and compared the resulting transcriptional signature with that of EWSR1-FLI1-silenced Ewing sarcoma cells. In accordance with the strong EGR2-induction by EWSR1-FLI1, both genes highly significantly overlap in their transcriptional signatures. Gene-set enrichment analyses (GSEA) and DAVID (Database for Annotation, Visualisation and Integrated Discovery) gene ontology analyses indicated a strong impact of EGR2 on cholesterol and lipid biosynthesis resembling its function in orchestrating lipid metabolism of myelinating Schwann cells. A673 and SK-N-MC Ewing sarcoma cells were transfected with specific siRNAs directed against EGR2 or EWSR1-FLI1 or non-targeting control siRNA. 48 h thereafter RNA was harvested and processed for microarray analysis.