Human embryonic stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE608 | GEO | 2004/01/19
SECONDARY ACCESSION(S): PRJNA85413
REPOSITORIES: GEO
Similar Datasets
Project description:Undifferentiated human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES3 and HES4 are proprietary human ES cell lines of ES Cell International Pte Ltd. Singapore. Keywords: other
2004-01-18 | E-GEOD-608 | biostudies-arrayexpress
Project description:A plethora of research has focused on the human embryonic stem cells (hESC) ever since they were first reported mainly due to their distinct features of self renewal and pluripotency. Probing of the hESC transcriptome using global expression profiling tools such as DNA microarray, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) and Expressed Sequence Tag (EST) analysis have contributed significantly in our current understanding of hESCs. In fact, a large number of markers to assess the pluripotent and differentiation status of hESCs have been presented by such studies. However, till date clarity is lacking in identifying a robust set of markers to assess the true state of the hESCs. In this paper, we report the generation of long SAGE libraries for partially differentiated and differentiated HES3 along with a deeper profiling of our previously reported HES3 undifferentiated library. Clustering analysis of these libraries in concert with long and short SAGE libraries available in public databases using Hierarchical Cluster Analysis (HCA) as well as a poison-based approach helped in identification of expression patterns distinct from those reported for the well established pluriptency/differentiation markers. Almost all the previous studies reporting a robust set of markers have focused on a gene by gene comparison in listing out the upregulated and downregulated genes rather than look at the expression patterns in establishing a list of markers. In this analysis, however, we report a new set of markers as well as add confidence to some previously reported markers based on their novel expression patterns as identified by SAGE analysis and also confirm it by real-time PCR analysis. For the real-time PCR confirmation, instead of taking two extreme data sets such as undifferentiated and a late stage embryoid body, we profiled a time series of embryoid body stages so that we could identify those genes which show a dramatic increase or decrease upon differentiation and hence would serve as more reliable markers. The hESC lines HES3 from ES Cell International, Singapore (http://www.escellinternational.com) were cultured on mouse embryonic fibroblast feeders (MEFs) as described previously. Selection of cells for library construction was done by micro-dissection following our established protocols. Spontaneous differentiation was induced by prolonged culture without changing the feeder layer. Briefly the HES3 cell line was grown to 18 passages (P18) on MEFs, after which no sub-culturing was performed. The medium was changed daily for 25 days and the differentiated cell population was harvested at the end of the culture period by micro-dissection. Cell differentiation was confirmed by Immuno-cytochemistry for markers to the three germ layers, as well as RT-PCR for the differentiation markers. For construction of the partially differentiated library, colonies which had started differentiation, as suggested by the morphological changes towards the centre and periphery of the colonies were used. Entire HES3 colonies (24P) which had started differentiation were harvested by micro-dissection and used for library construction. MmeI was used as tagging enzyme and libraries were constructed using the LS-SAGE kit from Invitrogen (http://www.invitrogen.com). Cloning of concatemerized ditags and sequencing of tags were done as outlined earlier. The 10 bp SAGE tags were extracted using Microsoft Excel for direct comparisons between libraries.
2010-02-17 | E-GEOD-12611 | biostudies-arrayexpress
Project description:Embryonic stem (ES) cells and ES cell-derived progeny characterized by nestin expression (including neural progenitors) were studied (three independent experiments). The mouse ES cell line R1 was cultured on a feeder layer of mouse embryonic fibroblasts (FL). ES cells were differentiated into nestin-positive cells for 4+8 days and 4+11 days according to the differentiation protocol by Rolletschek et al. (Mechanisms of Development 105, 93-104, 2001). The study was performed with three independent cell cultures (= triplicates). RNA was prepared from both undifferentiated ES cells and ES cell-derived nestin-positive cells, and from fibroblast feeder cells. Keywords = ES cell Keywords = nestin positive cells Keywords = feeder layer Keywords: other
2005-09-17 | GSE2375 | GEO
Project description:Sall4 is a mouse homolog of a causative gene of the autosomal dominant disorder known as Okihiro syndrome. We previously showed that Sall4 absence leads to lethality during peri-implantation and that Sall4-null embryonic stem (ES) cells proliferate poorly with intact pluripotency when cultured on feeder cells. However, a subsequent report indicated that shRNA-mediated Sall4 inhibition in ES cells led to a severe reduction in Oct3/4 and a secondary increase in Cdx2, which resulted in complete differentiation into the trophectoderm when cultured in the feeder-free condition. So we profiled gene expression changes when Sall4 is deleted in ES cells in the presence or absence of feeder cells. key word: embryonic stem (ES) cell, Sall4, feeder
2009-04-01 | GSE14219 | GEO
Project description:Sall4 is a mouse homolog of a causative gene of the autosomal dominant disorder known as Okihiro syndrome. We previously showed that Sall4 absence leads to lethality during peri-implantation and that Sall4-null embryonic stem (ES) cells proliferate poorly with intact pluripotency when cultured on feeder cells. However, a subsequent report indicated that shRNA-mediated Sall4 inhibition in ES cells led to a severe reduction in Oct3/4 and a secondary increase in Cdx2, which resulted in complete differentiation into the trophectoderm when cultured in the feeder-free condition. So we profiled gene expression changes when Sall4 is deleted in ES cells in the presence or absence of feeder cells. key word: embryonic stem (ES) cell, Sall4, feeder ES cells were cultured with or without mouse embryonic fibroblast (MEF) feeder cells in LIF-supplemented medium as described. To maintain the expression of Oct3/4, all ES cells were cultured in the presence of Blasticidin. Four samples were analyzed. GSM356329, GSM356330 : cultured in the absence of feeders GSM356331, GSM356332 : cultured on the feeders
2009-04-01 | E-GEOD-14219 | biostudies-arrayexpress
Project description:Tumor specimen samples from the multi-site, international, phase I advanced solid tumor ETC-159 clinical trial (NCT02521844, A*STAR Research Entities, Singapore), were analyzed using the PanCancer IO panel
2021-02-19 | GSE167039 | GEO
Project description:HES4 hESC were cultured in serum media and maintained on a layer of mouse embryonic fibroblast feeder cells at a density of 6 x 104 cells/cm2. For differentiation: hESC were differentiated for a total of 14 days. Differentiation was induced by passaging 4 human ES cell pieces onto 12 well plates seeded with 0.67 x 10E4 cells/cm2. Cells were maintained in media containing 20% FCS for 2 days before media containing 5% FCS was used. Reduced serum media was changed every second day for the remaining 12 days ESC cells were taken at time zero and RNA was isolated (hESC_undiff). Cells differentiated by the above procedure at day 14 were isolated and RNA extracted (Diff). The remaining cells were FACs sorted with antibodies to Podocalyxin, CD24 and GCTM-2. Two populations were isolated, 1: Positive for podocalyxin and CD24 and low level of expression of GCTM-2 (POD+CD24+GCTM2Low) and 2: Positive for podocalyxin and CD24 and negative for GCTM-2 (POD+CD24+GCTM2Neg). The experiment was repeated in triplicate. The final aim was to determine the gene expression enrichment in cells with the marker profile (Podocalyxin+, CD24+, GCTM-2-neg) which is predicted to be enriched for kidney precursors. Keywords: cell type comparison Three consecutive passages of HES4 cells were grown in standard conditions, RNA derived or differentiated for 14 days subject to FACs sorting, collection and RNA isolated. Microarray was performed on a total of 12 samples, (3 replicates of 4 populations).
2010-03-16 | E-GEOD-15257 | biostudies-arrayexpress
Project description:Embryonic stem (ES) cells and ES cell-derived progeny characterized by nestin expression (including neural progenitors) were studied (three independent experiments). The mouse ES cell line R1 was cultured on a feeder layer of mouse embryonic fibroblasts (FL). ES cells were differentiated into nestin-positive cells for 4+8 days and 4+11 days according to the differentiation protocol by Rolletschek et al. (Mechanisms of Development 105, 93-104, 2001). The study was performed with three independent cell cultures (= triplicates). RNA was prepared from both undifferentiated ES cells and ES cell-derived nestin-positive cells, and from fibroblast feeder cells.
2008-06-12 | E-GEOD-2375 | biostudies-arrayexpress
Project description:The purpose of the study was to identify transcriptomic changes between feeder-free ES and XEN cells. ES cells were cultured feeder-free on 0.1% gelatin in 2iLIF in N2B27 media. XEN cells were also cultured feeder-free on 0.1% gelaton in RPMI1640 supplemented with 15% FBS, 2mM GlutaMAX and BME.
2020-10-22 | GSE159855 | GEO
Project description:HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3’s role in neurogenesis. To further investigate how HES3 functions during development, we generated a zebrafish CRISPR/Cas9 knockout of her3, the zebrafish ortholog of HES3. Zebrafish her3 mutants are not embryonic lethal and as adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants are significantly smaller than wildtype and present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 knockout embryos are enriched for HOX and sox10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts.
2023-01-16 | GSE196814 | GEO