Project description:Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells. This SuperSeries is composed of the following subset Series: GSE4075: Neural induction (Embrioid bodies-Retinoic acid) GSE4076: Neural induction (N2B27 monolayer cluture) GSE4077: ES, EC, NS, TS, Placenta and Neural induction (N2B27) comaprison Keywords: SuperSeries Refer to individual Series
Project description:This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org). The experiment was conducted at University of Cologne, Cologne, Germany. Goal of the experiment is the identification of genes involved in endothelial differentiation. This is of great interest for the understanding of the cellular and molecular mechanisms involved in the development of new blood vessels. Mouse embryonic stem (mES) cells serve as a potential source of endothelial cells for transcriptomic analysis. We isolated endothelial cells from 8-days old embryoid bodies by immuno-magnetic separation using platelet endothelial cell adhesion molecule-1 (also known as CD31) expressed on both early and mature endothelial cells.
Project description:This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org). The experiment was conducted at University of Cologne, Cologne, Germany. Goal of the experiment was an analysis the transcriptome of the ES-cell derived pure T-brachyury expressing CGR8 cells. Materials and methods: On day 0, EBs were made from T-brachyury ES (CGR8) cell line by hanging drop protocol. On second day, the hanging drop EBs were transferred into suspension. On third day, the EBs were treated or untreated with puromycin at a concentration of 5ug/ml for 2 days. On 5th day, the medium was changed and added medium with or without puromycin at a concentration of 2 ug/ml for 1 day. On day 6th , RNA was isolated from EBs treated or untreated with puromycin for affymetrix analysis.
Project description:Retinoic Acid Receptors (RARs) bind RA-response elements in regulatory regions of their target genes. While canonical RAREs comprise direct repeats of the consensus 5’-RGKTCA-3’ sequence separated by 1, 2 or 5 nucleotides (DR1, DR2, DR5), we show that shortly after RA treatement of mouse embryoid bodies or F9 cells, RARs occupy a large repertoire of DR0, DR2, DR5, DR8 and IR0 elements. In vitro, RAR-RXR bind these non-canonical spacings with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half sites with DR2 and DR0 spacings. This specific half site organisation constitutes a previously unrecognised, but frequent signature of RAR binding elements and acts as an RARE. At later stages of embryoid body differentiation, RARs relocalise to a restricted repertoire of sites comprising predominantly DR5 elements. Differentiation thus involves genomic relocalisation of RARs, and a switch from DR0 and DR8 at early times to DR5 at later stages. Examination of genomic localisation of RAR in differentiating embryoid bodies.
Project description:We aim to understand the role that Cdx2 plays in specifying the rostro-caudal identity of differentiating motor neurons. We find that expressing Cdx2 in combination with FGF signaling is sufficient to produce motor neurons with a more caudal identity. ChIP-seq analysis of Cdx2 finds that it binds extensively throughout the Hox regions in progenitor motor neurons. Analysis of polycomb-associated chromatin over Hox regions in the subsequently generated motor neurons finds that Cdx2 binding corresponds to chromatin domains encompassing de-repressed caudal Hox genes. These results suggest a direct role for Cdx2 in specifying caudal motor neuron identity. Expression studies: Affymetrix arrays are used to profile gene expression in ES cells, RA/Hh-derived Day 5 motor neurons, and RA/Hh-derived motor neurons that have also been exposed to Dox (to activate iCdx2) and FGF.
Project description:We used microarrays to detail the global programme of gene expression in embryonic stem cells, early differentiated embrioid bodies and effect of short-term ATRA treatment. Expression data from undifferentiated mouse embryonic stem cells (D3), four-day old aggregated embrioid bodies and 12h atRA or DMSO treated embrioid bodies. Three replicates each.
Project description:In this experiment, we sought to analyze how the transcriptome of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons 3 lines (WT, Δ5|6, Δ5|6:7|9)
Project description:In this experiment, we sought to identify how the distribution of CTCF, H3K27me3, H3K4me3, Pol II, H2AK119Ub1, EZH2 3 lines (WT, Δ5|6, Δ5|6:7|9)
Project description:Myogenic differentiation relies on Pax7 function. We used embryonic stem cells lacking functional Pax7 to follow its role in derivation of skeletal myoblasts. Microarray analysis allowed us to compare transcriptomes of undifferentiated and differentiating embryonic stem cells of two genotypes, i.e. Pax7+/+ and Pax7-/- at day 7 and 21 of culture. Undifferentiated mouse embryonic stem cells, embryiod bodies at day 7, and embryoid body outgrowths at day 21 of differentiation were collected for RNA extraction and hybridization on Affymetrix microarrays.