Mammalian genome : official journal of the International Mammalian Genome Society 20040101 1
Expression profiling offers a potential high-throughput phenotype screen for mutant mouse embryonic stem (ES) cells. We have assessed the ability of expression arrays to distinguish among heterozygous mutant ES cell lines and to accurately reflect the normal function of the mutated genes. Two ES cell lines hemizygous for overlapping regions of mouse Chromosome (Chr) 5 differed substantially from the wildtype parental line and from each other. Expression differences included frequent downregulati ...[more]
Project description:Loss of imprinting (LOI), commonly observed in human tumors, refers to loss of monoallelic gene regulation normally conferred by parent-of-origin specific DNA methylation. To test the function of LOI in tumorigenesis, we developed a model using transient demethylation to generate imprint-free mouse embryonic stem (IF-ES) cells. To analyse the effect of LOI on gene expression, we compared gene expression profiles from embryonic fibroblasts derived from IF-ES cells (IF-MEFs) and wildtype MEFs.
Project description:The bHLH transcription factor Tfe3 is a powerful regulator of pluripotency and we report a genome-wide analysis of Tfe3 occupancy in mouse ES cells. Nuclear localization of Tfe3 is inhibited by a protein complex containing the tumor-suppressor Folliculin (Flcn) and we also determine Tfe3 binding sites in ES cells expressing an shRNA targeting Flcn. Specificity is controlled for by using unspecific IgGs and ES cells expressing an shRNA targeting Tfe3. ChIP-Seq profiling of Tfe3 in ES cells
Project description:This SuperSeries is composed of the following subset Series: GSE26451: Transcriptome data for human ES, FORESKIN and FORESKIN-derived iPS (ES4SKIN) cells GSE26453: Transcriptome data for human ES, IMR90 and IMR90-derived iPS (ESIMR90) cells Refer to individual Series
Project description:Our understanding of the biology of embryonic stem (ES) cells is deeply rooted in characterization of their transcriptomes, epigenetics and underlying gene regulatory networks. There is evidence that post-transcriptional processes such as signaling, adhesion, protein turnover and post translational modifications make a significant contribution to regulating the balance between self-renewal and differentiation, and it is therefore necessary to also characterize ES cells at the protein level. In this experiment, we used a workflow termed hyperLOPIT (hyperplexed localization of organelle proteins by isotope tagging) to characterize the subcellular distribution of proteins in a population of self-renewing E14TG2a mouse ES cells. Over 5,000 protein groups were quantified in both of the two replicates, enabling characterization of protein localization to organelles (including sub-nuclear resolution), cell surface, cytoskeleton and cytosol. The steady-state localization of transitory proteins, protein complex constituents, and signaling cascades could also be mapped.
Project description:To study the function of BAF250 during ES cell self renewal and differentiation Experiment Overall Design: wild type,BAF250 heterozygous, and BAF250 homozygous ES cells were analyzed
Project description:Successful derivation of a specific cell lineage from pluripotent stem cells will tremendously facilitate the clinical usage of pluripotent stem derived somatic cells. Herein, we demonstrate that ER71/Etv2, GATA2 and Scl form a core network in hemangioblast development and that transient co-expression of these three factors robustly induced hemangioblasts from ES cells. Such induced hemangioblasts potently generated hematopoietic and endothelial cells in culture as well as in vivo, warranting the evaluation of these cells in the future for repairing and/or regenerating hematopoietic and/or angiogenic defects. We have established a doxycycline inducible ES cell, iEGS, in which ER71/Etv2, GATA2 three transcription factors can be transiently co-expressed by doxycycline induction. We further analyzed the downstream target genes and signaling pathways at 6, 12 and 24hrs after ER71/Etv2, GATA2 induction. These data were obtained from three independent experiments.
Project description:We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression. Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.
Project description:Gene expression profiling reveals that SET1A regulates gene expression, metabolism and development programs in mouse ES Cells To analyze the global effect of SET1A on gene expression in ES cells, we compared the gene expression profiles in CGR8 cells treated with control and Set1A siRNA by RNA-seq.
Project description:ES cells are able to self-renew and remain pluripotent. These characteristics are maintained by both genetic and epigenetic regulators. Protein arginine methyltransferase (PRMT) 4 and 5 are shown to be important in early embryonic development and in ES cells. PRMT6-mediated di-methylation of histone H3 at arginine 2 (H3R2me2) can antagonize the tri-methylation of histone H3 at lysine 4, which marks active genes. However, it is unclear whether PRMT6 and PRMT6-mediated H3R2me2 play crucial roles in early embryonic development and ES cell identity. In this study, we investigate their functions using mouse ES cells as the model. We used microarray (Affymetrix GeneChip Mouse Gene 1.0ST) to examine the global change of gene expression in mouse ES cells when Prmt6 was overexpressed and identified distinct classes of genes that are up-regulated and down-regulated during this process. Mouse ES cells were transfected with either pCAGIP.puro empty vector (control) or Prmt6 overexpressing plasmid (P+6 OE). After 3 days of selection by puromycin, cells from both populations were subjected to RNA extraction and hybridization on Affymetrix microarrays.