Expression profile of MEFs, iPS, and ES in different culture condition
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE24861 | GEO | 2010/10/27
SECONDARY ACCESSION(S): PRJNA133413
REPOSITORIES: GEO
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Project description:MEFs can be reprograming to ES by defined reprogramming factors, the derived ES-like cells were termed iPSc. Completely reprogrammed iPSc have identifed gene expression profle with ES. Culture condition may influent the pluripotency of iPSCs.iPS/ES cultured in differient ES medium may have different gene expression profile. We preform an experiment to analyze the gene expression difference among MEFs cultured in FBS and iCD1,iPSc cultured in KSR medium and N2B27 supplementary with 2i medium , and ES cultured in N2B27 supplementary with 2i medium.
2010-10-27 | E-GEOD-24861 | biostudies-arrayexpress
Project description:Transcriptional profiling of Mouse iPS cells and MEFs comparing ES cells. RNA was prepared from the ES cell line CGR8.8, MEFs and and iPSC clone and cRNA was hybridized to Agilent Whole Murine Genome Oligo Microarray.
2011-07-01 | E-GEOD-22327 | biostudies-arrayexpress
Project description:Transcriptional profiling of Mouse iPS cells and MEFs comparing ES cells.
2011-07-01 | GSE22327 | GEO
Project description:Mefs were transduced with Oct4 , Sox2, Klf4 and c-myc to induce pluripotency. The histone H3 K4 and H3 K27 trimethylation status was compared genome wide in ES cells, MEFs, and induced pluripotent cells (iPS). Keywords: ChIP-Chip
2007-05-23 | GSE7815 | GEO
Project description:It is well-known that embryonic stem cells (ESC) are much more sensitive to replication-induced stress than differentiated cells but the underpinning mechanisms are largely unknown. H2A.X, a minor variant of H2A, constitutes only 1-10% of the mammalian genome. H2A.X plays a well-known for role in the DNA damage response and maintaining stability in the genome, including the regions frequently experiencing replication stress, such as the fragile sites. Intriguingly, several recent studies have reported that H2A.X function is elevated in ESC; and others reported that H2A.X function is provoked during cellular reprogramming (in induced pluripotent stem cells, iPSC), indicating that increased proliferation during iPS may trigger replication stress and the H2A.X DNA damage response. However, several studies of genomic instability in iPSC led to different conclusions on this important issue. For example, frequent copy number variants (CNV) were reported at the genomic regions sensitive to replication stress, such as the fragile sites. On the other hand, another study reported the lack of genomic instability in mouse iPS clones that are able to generate “all-iPS” animals in tetraploid complementation assays (4N+ iPSC), indicative of a potential link between pluripotency and genome integrity. However, whether if high level genomic instability occurs in the 4N- iPSC iPSC clones at replication stress sensitive regions is unknown. Moreover, due to the lack of mechanistic insights on genome integrity maintenance, how pluripotency and genome integrity are connected remains elusive. Here we show that H2A.X plays unexpected roles in maintaining pluripotency and genome integrity in ESC and iPSC. In ESC, it is specially enriched at genomic regions sensitive to replication stress so that it protects genome integrity thereat. Faithful H2A.X deposition is critical for genome integrity and pluripotency in iPSC. H2A.X depositions in 4N+ iPSC clones faithfully recapitulate the ESC pattern and therefore, prevent genome instability. On the other hand, insufficient H2A.X depositions in 4N- iPSC clones at such regions lead to genome instability and defects in replication stress response and DNA repair, reminiscent of the H2A.X deficient ESC. In this study, male 129sv/C57 ES cell genomic DNA was used as reference control, to identify CNV sites in iPS cell lines. And also detect H2A.X (-/-) ES cell (129/Sv) CNVs, with the H2A.X(f/f) ES cell DNA (129/Sv) as control. DNA samples were compared on NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9).
2014-09-07 | E-GEOD-42266 | biostudies-arrayexpress
Project description:WT TR MEFs and Keap1–/– TR MEFs were established according to the following method. Keap1+/– mice were mated, and WT and Keap1–/– embryos were collected at embryonic day 13.5. Primary MEFs were immortalized by expression of SV40 T antigen. The immortalized MEFs were transformed by expression of HRAS G12V to generate WT TR MEFs and Keap1–/– TR MEFs.
2017-05-06 | GSE98594 | GEO
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.
2005-10-20 | E-MEXP-450 | biostudies-arrayexpress
Project description:To investigate how mammalian Ssu72 regulated gene expression, we performed RNA-Seq analyses of Ssu72 in three different cell types depending on their proliferation capabilities: embryonic stem (ES) cells (highly proliferating), primary murine embryonic fibroblasts (MEFs) (moderate proliferating), and hepatocytes (almost quiescent). Ssu72 deletion was induced by infection with Cre recombinase adenovius (Ad-Cre). Infection of ESf/f, MEFf/f, and hepatocytef/f with Ad-Cre resulted in efficient reduction of Ssu72 levels. Depletion of Ssu72 resulted in downregulation or upregulation of large subsets of genes in three different cell types.
2020-12-28 | GSE122101 | GEO
Project description:In this study we have compared functional and molecular properties of highly purified murine induced pluripotent stem (iPS) cell- and embryonic stem (ES) cell-derived cardiomyocytes (CM). In order to obtain large amounts of purified CM, we have generated a transgenic murine iPS cell line, which expresses puromycin resistance protein N-acetyltransferase and EGFP under the control of the cardiomyocyte-specific α-myosin heavy chain promoter (alphaMHC-Puro-IRES-GFP, aPiG). We demonstrate that murine aPIG-iPS and aPIG-ES cells differentiate into spontaneously beating CM at comparable efficiencies. When selected with puromycin both cell types yielded more than 97% pure population of CMs. Both aPIG-iPS and aPIG-ES cell-derived CM express typical cardiac transcripts and structural proteins and possess similar sarcomeric organization. Action potential recordings revealed that iPS- and ES cell-derived CM respond to beta-adrenergic and muscarinic receptor modulation, express functional voltage-gated sodium, calcium and potassium channels and possess comparable current densities. Comparison of global gene expression profiles of CM generated from iPS and ES cells revealed that both cell types cluster close to each other but are highly distant to undifferentiated ES or iPS cells as well as unpurified iPS and ES cell-derived embryoid bodies (EB). Both iPS and ES cell-derived CMs express genes and functional categories typical for CM. They are enriched in genes involved in transcription and genes coding for structural proteins involved in cardiac muscle contraction and relaxation. They also express genes involved in heart and muscle developmental processes, ion export and ion binding processes and various metabolic processes for ATP synthesis. These CMs downregulate genes involved in immune response, cell cycle and cell division, thus demonstrating the CMs population is mitotically inactive. Most surface signaling pathways are also downregulated. Thus, a transgenic aPiG-iPS cell line can provide a robust supply of highly purified and functional CMs for future in vitro and in vivo studies.
2012-12-01 | GSE18514 | GEO
Project description:Purposes: (1) compare the SUMO chromatin landscape between mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESc) (2) Decipher how hyposumoylation enhances MEF to induced pluripotent stem cells (iPSc) reprogramming (3) Decipher how hyposumoylation enhances ESc to 2C-like cells conversion. Methods : (1) ChIP-seq in MEFs and ESc for SUMO isoforms and histone marks. (2) ChIP-seq for transcription factors and histone marks at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). ATAC-Seq at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). RNA-Seq in MEFs, iPSc, at day 4 and day 7 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). (3) RNA-Seq in ESc comparing wild-type (siCtrl) and hyposumoylated cells (siUbc9). Results: (1) SUMO chromatin landscape is highly different between MEFs and ESc and associates to distinct chromatin marks. (2) Hyposumoylation enhances MEFs to iPSc reprogramming by favoring the extinction of the MEF transcriptional program and redistributing pluripotency factors from MEF enhancers toward ES enhancers. (3) Hyposumoylation enhances ES to 2C-like conversion by destabilizing heterochromatin thus resulting in an activation of the 2-cell transcriptional program. Conclusion: SUMO at chromatin is gate-keeper of cell-identity.
2018-10-24 | GSE99009 | GEO