Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA146305 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To identify potential Elongin A targets during neuronal differentiation of ES cells, a cDNA microarray analysis comparing embryoid bodies (EBs) derived from Elongin A+/+ ES cells and Elongin A-/- ES cells was performed. Gene expression in EBs derived from Elongin A+/+ and Elongin A-/- ES cells was measured at day 4 after retinoic acid treatment (2 ?M).
2011-07-25 | E-GEOD-30911 | biostudies-arrayexpress
Project description:To identify potential Elongin A targets during neuronal differentiation of ES cells, a cDNA microarray analysis comparing embryoid bodies (EBs) derived from Elongin A+/+ ES cells and Elongin A-/- ES cells was performed.
2011-07-26 | GSE30911 | GEO
Project description:S6K1 Knockout mice has a lean phenotype and resitant to a High Fat Diet-induced obesity (Um S.H., Nature, 2004). Adipocyte differentiation consists of two step, first, commitment from stem cell to adipocyte progenitors and second, terminal differentiation from adipocyte progenitors to mature adipocyte. We studied S6K1-dependent gene expression regulation in early stage of commitment by employing ES cell(ESC)-Embryoid Bodies(EBs) differentiation model. We established stable ES cell lines infected with either control non-silencing shRNA (shNS) or S6K1 targetting shRNA (shS6K1). Each sample was treated with retinoic acid for 3 days to induce adipogenesis, then gene expression profile was analyzed employing microarrays and up-regulated and down-regulated genes were selected for analysis. Mouse Embryoid Bodies (approximately 1000 EBs per sample) were treated with retinoic acid (1µM) for 3 days then collected for RNA extraction and hybridization on Affimetrix microarray. Two biological replicates were each performed for EBs prepared from either shNS ESCs or shS6K1 ESCs.
2010-05-14 | E-GEOD-20349 | biostudies-arrayexpress
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 Aventis Pharma, Paris, France. Goal of the experiment is the characterisation of gene expression profile during neuronal differentiation of Sox1Tv2 ES cells in the embryoid body protocol. Materials and methods:Sox1Tv2-E14 derived ES cells have been cultured without serum in liquid culture in order to form embryoid bodies. A 48 hour retinoic acid stimulation has been applied between days 4 and 6 (EB6) for half the samples. After 8 days of differentiation (EB8), EBs have been dissociated and cells plated on poly-D-lysine/laminin coated dishes and cultured in differentiation medium. bFGF has been added to the culture medium during the first 2 days after plating (N2). After removal of bFGF, cells were allowed to differentiate for 4 more days (N6). Protocol described in FunGenES handbook. Relationships between samples: Different time points during differentiation process: ES, EB3, EB4, EB6 (ctl and RA), EB8 (ctl and RA), N2 (ctl and RA), N6 (ctl and RA),Treatments: Retinoic acid treatment: EB4 to EB6bFGF addition (10ng/ml final): postplating to N2. Culture conditions: Liquid medium culture: GMEM + KOSR Differentiation medium: DMEM/F12 and NBM medium with N2 and B27 supplements.
2009-07-10 | E-TABM-669 | biostudies-arrayexpress
Project description:This experiment was specifically designed to measure neural targets of Shh signaling, we sought to profile the genes upregulated by Hh signaling in the ventral neural tube to obtain a valid dataset. To obtain ventral-specific markers, we generated retinoic acid-treated EBs grown in the presence or absence of HH-Ag. We did not observe induction of ventral Hh markers in RA-treated constitutive Gli1FLAG EBs and used these for the control, baseline set. The presence of FoxA2, Nkx2.9 and Nkx6.1 amongst the top 10 genes based on expression levels suggests that profiling significantly enriches for Hh-dependent cell types. As expected, the benchmark standard Gli1 was not up-regulated in our array, since it is constitutively expressed in the control as well. Keywords: neural progenitors, embryoid bodies, differentiation, Hedgehog, retinoic acid
2007-04-20 | GSE4936 | GEO
Project description:These data include the genome wide location of different histone modifications by ChIP sequencing in mouse ES cells, and RNA Seq data generated from wild type and EED KO mouse ES cells and knocked down for unrelated protein and Setd2 protein. ChIP-Seq: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type mouse E14 ES cells, wild type E36 ES cells, EED KO E36 ES cells, wild type Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO) using specific antibody against different histone modifications. RNA-Seq: Total RNA extracted from wild type E36 ES cells, EED KO E36 ES cells, wild type E36 Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO), E14 Ctrl KD, E14 Setd2 KD.
2013-12-05 | E-GEOD-51006 | biostudies-arrayexpress
Project description:HOXB4 target genes in ES cell-derived embryoid bodies (EBs)
| PRJNA102549 | ENA
Project description:Occupancies of promoters by TBP, PolII, TFIIB as well as chromatin marks H3K4Me3 and H3K27ac were compared in embryonic stem cells (ESC) and in embryoid bodies (EB) treated with retinoic acid (RA) derived from the WT and Taf4a-/- lineages. Reduced occupancies for these factors and decreased signals for H3K4Me3 and H3K27ac were observed for genes associated with neuronal differentiation in EB of Taf4a-/- line compared to EB of WT line.
2016-03-20 | GSE70661 | GEO
Project description:S6K1 Knockout mice has a lean phenotype and resitant to a High Fat Diet-induced obesity (Um S.H., Nature, 2004). Adipocyte differentiation consists of two step, first, commitment from stem cell to adipocyte progenitors and second, terminal differentiation from adipocyte progenitors to mature adipocyte. We studied S6K1-dependent gene expression regulation in early stage of commitment by employing ES cell(ESC)-Embryoid Bodies(EBs) differentiation model. We established stable ES cell lines infected with either control non-silencing shRNA (shNS) or S6K1 targetting shRNA (shS6K1). Each sample was treated with retinoic acid for 3 days to induce adipogenesis, then gene expression profile was analyzed employing microarrays and up-regulated and down-regulated genes were selected for analysis.
2010-02-17 | GSE20349 | GEO
Project description:Embryonic stem cells (ESC) are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass in their developmental potential. ESCs pluripotency is maintained through a complex interplay of different signaling pathways and a network of transcription factors, which is centered around Oct3/4, Sox2 and Nanog. Although, in general, much is known about this pluripotency self-renewal circuitry, the molecular events that lead ESC to exit from pluripotency and begin differentiation are currently less known. Retinoic acid, an active metabolite of the vitamin A (retinol), plays important and pleiotropic roles in vertebrate embryonic development and ESC differentiation. Here we demonstrate that RA promotes early steps of ESC differentiation, and that ESC increase their capacity to synthesize RA during spontaneous differentiation as embryoid bodies, up-regulating the RA biosynthetic pathway components RDH1, RDH10, ADH3, RALDH2, and CRABP2. Microarray derived from total RNA of mESC not treated or treated with all-trans retinoic acid (ATRA) for 2 hours.
2016-02-10 | E-GEOD-66043 | biostudies-arrayexpress