E-TABM-672
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ABSTRACT:
PROVIDER: E-TABM-672 | ExpressionAtlas | 2015-11-02
REPOSITORIES: ExpressionAtlas
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Project description:time-course experiment with embryoid bodies of CGR8 mouse embryonic stem cells ; in the whole time-series RNA from 0 days old embryoid bodies were hybridized against RNA from 3 days and 10 days old embryoid bodies Keywords = embryoid bodies Keywords = mouse Keywords = time-course Keywords = oligonucleotide array Keywords: time-course
2006-04-01 | GSE2469 | GEO
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 RNA expression profiling in the first 10 days of differentiation in CGR8 cells. Materials and methods: CGR8 cells were cultivated as EBs without addition of selective reagents in hanging drop cultures in a timecourse experiment. After 7 days, EBs were plated in gelatin-coated 6-well plates. RNA was prepared from ES cells (day 0), EBs (day 1 to 7) and plated EBs (day 10). Culture conditions: ES cells were differentiated via hanging drop protocol into embryoid bodies. RNA isolation method: The RNA isolation was carried out following standard methods (on column, RNeasy Mini kit, Qiagen)
2009-07-10 | E-TABM-672 | biostudies-arrayexpress
Project description:16 embryonic stem cell (ESC) samples (8 groups in duplicate) were processed for microarray analysis using the Affymetrix Mouse Genome 430 2.0 GeneChip. The samples included the parental Ainv15 ESC line (1) undifferentiated (Ainv15 ESC), (2) differentiated for 3 days as embryoid bodies (Ainv15 EB3) or (3) for 10 days as embryoid bodies (Ainv15 EB10). The remaining samples included tetracycline inducible Ngn3 ESC line derived from the parental Ainv15 ESC line (4) after differentiation and addition of doxycycline for 3 days without embryoid body formation (Ngn3 ES3 ON), (5 and 6) after differentiation as embryoid bodies for 3 days with (Ngn3 EB3 ON) or without (Ngn3 EB3 OFF) doxycycline, and (7 and 8) after differentiation as embryoid bodies for 10 days with (Ngn3 EB10 ON) or without (Ngn3 EB10 OFF) doxycycline.
2007-06-29 | E-CBIL-29 | biostudies-arrayexpress
Project description:Embryonic stem cells studies have generated a great interest due to their ability to form a wide variety of matured cells. However, there remains a poor understanding of mechanisms regulating the cell state of ESCs and of the genes they express during early differentiation. Gene expression analysis may be a valuable tool to elucidate either the molecular pathways involved in self-renewal and pluripotency or early differentiation and to identify potential molecular therapy targets. The aim of this study was to characterize at molecular level the undifferentiated mouse ESCs state and the early development towards embryoid bodies. To attemp this issue we performed CodeLink Mouse Uniset I 20K bioarrays in a well-characterized mouse ESC line, MES3, 3- and 7 day-old embryoid bodies and we compared our findings with those in adult tissue cells. Gene expression results were subsequently validated in a commercial stem cell line, CGR8 (ATCC). SAM analysis was used to identify statistically significant changes in microarray data. We identified 3664 genes expressed at significantly greater levels in MES3 stem cells than in adult tissue cells, which included 611 with 3-fold higher gene expression level versus the adult cells. We also investigated the gene expression profile during early embryoid body formation, identifying 2040 and 2243 genes that were up-regulated in 3- and 7-day-old EBs, respectively. Our gene expression results in MES3 cells were partially confirmed in CGR8 cells, showing numerous genes that are expressed in both mouse stem cells. In conclusion, our results suggest that commonly expressed genes may be strong candidates for involvement in maintenance of a pluripotent and undifferentiated phenotype and in early development. This study characterizes at molecular level the undifferentiated mouse ESCs state and the early development towards embryoid bodies. We identified numerous genes not been previously reported, which may offer novel insights into the behaviour of mouse ESC, the maintenance of their undifferentiated state and the mechanisms underlying their pluripotency, self-renewal and early differentiation.
2010-11-17 | E-GEOD-25403 | biostudies-arrayexpress
Project description:Expression of the proendocrine gene neurogenin 3 (Ngn3) is required for the development of pancreatic islets. In order to better characterize the molecular events regulated by Ngn3 during development, we have determined the expression profile of differentiating murine embryonic stem cells (mESCs) uniformly induced to overexpress Ngn3. An ESC line was created that allows for the induction of Ngn3 by adding doxycycline (Dox) to the culture medium. Genome-wide microarray analysis was performed to identify genes regulated by Ngn3 in a variety of both undifferentiated and differentiated conditions. Characterization of pancreatic developmental markers during embryoid body (EB) formation revealed an optimum context for Ngn3 induction. Neuroendocrine genes including neurogenic differentiation 1 (NeuroD1) and single minded 1 (Sim1) were found to be significantly upregulated. Genes regulated by Ngn3 independent of the context were analyzed using systematic gene ontology tools and revealed Notch signaling as the most significantly regulated signaling pathway (p=0.009). This result is consistent with the hypothesis that Ngn3 expression makes the cell competent for Notch signaling to be activated and conversely, more sensitive to Notch signaling inhibition. Indeed, EBs induced to express Ngn3 were significantly more sensitive to gamma-secretase inhibitor-mediated Notch signaling inhibition (p<0.0001). Moreover, we find that Ngn3 induction in differentiating ESCs results in significant increases in insulin, glucagon, and somatostatin transcription. Experiment Overall Design: 16 embryonic stem cell (ESC) samples (8 groups in duplicate) were processed for microarray analysis using the Affymetrix Mouse Genome 430 2.0 GeneChip. The samples included the parental Ainv15 ESC line (1) undifferentiated (Ainv15 ESC), (2) differentiated for 3 days as embryoid bodies (Ainv15 EB3) or (3) for 10 days as embryoid bodies (Ainv15 EB10). The remaining samples included tetracycline inducible Ngn3 ESC line derived from the parental Ainv15 ESC line (4) after differentiation and addition of doxycycline for 3 days without embryoid body formation (Ngn3 ES3 ON), (5 and 6) after differentiation as embryoid bodies for 3 days with (Ngn3 EB3 ON) or without (Ngn3 EB3 OFF) doxycycline, and (7 and 8) after differentiation as embryoid bodies for 10 days with (Ngn3 EB10 ON) or without (Ngn3 EB10 OFF) doxycycline.
2007-12-01 | E-GEOD-3653 | biostudies-arrayexpress
Project description:Embryonic stem cells studies have generated a great interest due to their ability to form a wide variety of matured cells. However, there remains a poor understanding of mechanisms regulating the cell state of ESCs and of the genes they express during early differentiation. Gene expression analysis may be a valuable tool to elucidate either the molecular pathways involved in self-renewal and pluripotency or early differentiation and to identify potential molecular therapy targets. The aim of this study was to characterize at molecular level the undifferentiated mouse ESCs state and the early development towards embryoid bodies. To attemp this issue we performed CodeLink Mouse Uniset I 20K bioarrays in a well-characterized mouse ESC line, MES3, 3- and 7 day-old embryoid bodies and we compared our findings with those in adult tissue cells. Gene expression results were subsequently validated in a commercial stem cell line, CGR8 (ATCC). SAM analysis was used to identify statistically significant changes in microarray data. We identified 3664 genes expressed at significantly greater levels in MES3 stem cells than in adult tissue cells, which included 611 with 3-fold higher gene expression level versus the adult cells. We also investigated the gene expression profile during early embryoid body formation, identifying 2040 and 2243 genes that were up-regulated in 3- and 7-day-old EBs, respectively. Our gene expression results in MES3 cells were partially confirmed in CGR8 cells, showing numerous genes that are expressed in both mouse stem cells. In conclusion, our results suggest that commonly expressed genes may be strong candidates for involvement in maintenance of a pluripotent and undifferentiated phenotype and in early development.
2010-11-17 | GSE25403 | GEO
Project description:Cell line R1 (Mouse embryonic stem cell line) was cultured on 3 different conditions for differentiation study. The experiment ran for 7 days and samples were taken every 24hrs. Afterward, samples on days 0,3,5 and 7 were processed for microarray analysis. The conditions were the differentiation of the stem cells for 7 days through a)formation of embryoid bodies, b)culture on a gelatin coated surface and c) culture on a matrigel coated surface. Keywords: Time course
2008-03-28 | GSE8574 | GEO
Project description:Cell line R1 (Mouse embryonic stem cell line) was cultured on 3 different conditions for differentiation study. The experiment ran for 7 days and samples were taken every 24hrs. Afterward, samples on days 0,3,5 and 7 were processed for microarray analysis. The conditions were the differentiation of the stem cells for 7 days through a)formation of embryoid bodies, b)culture on a gelatin coated surface and c) culture on a matrigel coated surface. Experiment Overall Design: 10 samples, considering: days 3, 5 and 7 for each of the 3 differentiating conditions and one for day zero. Technical replicates were made every three sample points. 3 Complete biological replicates were performed.
2008-06-16 | E-GEOD-8574 | biostudies-arrayexpress
Project description:In order to identify cells expressing RUNX1c during hematopoietic differentiation of human embryonic stem cells (hESCs), we targeted GFP downstream of the RUNX1 distal promoter. GFP was observed from 10-25 days of embryoid body differentiation and accurately mirrored expression of the endogenous RUNX1c isoform. GFP was restricted to CD45+ hematopoietic cells and GFP+CD34+ cells were highly enriched for progenitor cells. Appearance of the first wave of hematopoietic blast colony forming cells (Bl-CFC) in d3-4 embryoid bodies, antedated the expression of RUNX1c. These results confirm a role for RUNX1c in marking a second wave of hematopoietic progenitor cells in differentiating hESCs. The purpose of the cord blood samples was to perform comparison of them to the gene expression profiles of the Runx fractions - as the cord blood represents a heterogeneous mix of hematopoietic stem cells and multipotent progenitors cells.
2012-02-12 | E-MEXP-3356 | biostudies-arrayexpress
Project description:Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development is not established. We have generated Tet1/2/3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential. Combined deficiency of all three Tets depleted 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies (EBs) and teratomas. Consistent with impaired differentiation, TKO-ESCs contributed poorly to chimeric embryos and could not support embryonic development. Global gene expression and methylome analyses of TKO-EBs revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet- and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of ESCs and development. To quantify global gene expression in differentiating embryoid bodies (EBs) derived from wild type (WT) and Tet triple knockout (TKO), TKO and WT mouse embryonic stem cells (ESCs) were differentiated in vitro to EBs and cultured for 10 days. RNA was extracted using Qiagen RNeasy kit and subjected to microarray analysis. Global gene expression profile of two technical replicas of WT embryoid bodies (2 samples in total) was compared to two technical replicas of two independent TKO embryoid bodies (4 TKO samples in total).
2014-04-14 | E-GEOD-55574 | biostudies-arrayexpress