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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide analysis of pluripotency marker expression of ESKM-iPS cells

ABSTRACT: iPS cells, produced in in presence of exogeneously expressed E-cadherin and abcence of viral Oct4 were compared with conventional produced OSKM-iPS cells and murine embryonic stem cells (mESCs) or MEFs Total RNA was isolated from iPSCs and mESCs grown in presence of LIF on gelatin-coated plates for 4 days and from murine embryonic fibroblasts grown in standard medium (DMEM-Glutamax, high-glucose, 10 % FBS, 1X non-essential amino acids, penicillin/ streptomycin

ORGANISM(S): Mus musculus

SUBMITTER: Torben Redmer

PROVIDER: E-GEOD-28594 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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E-cadherin is crucial for embryonic stem cell pluripotency and can replace OCT4 during somatic cell reprogramming.

Redmer Torben T Diecke Sebastian S Grigoryan Tamara T Quiroga-Negreira Angel A Birchmeier Walter W Besser Daniel D

EMBO reports 20110701 7

We report new functions of the cell-adhesion molecule E-cadherin in murine pluripotent cells. E-cadherin is highly expressed in mouse embryonic stem cells, and interference with E-cadherin causes differentiation. During cellular reprogramming of mouse fibroblasts by OCT4, SOX2, KLF4 and c-MYC, fully reprogrammed cells were exclusively observed in the E-cadherin-positive cell population and could not be obtained in the absence of E-cadherin. Moreover, reprogrammed cells could be established by vi ...[more]

PMID: 21617704

Similar Datasets

Genome-wide analysis of pluripotency marker expression of ESKM-iPS cells

Project description:iPS cells, produced in in presence of exogeneously expressed E-cadherin and abcence of viral Oct4 were compared with conventional produced OSKM-iPS cells and murine embryonic stem cells (mESCs) or MEFs

2011-04-14 | GSE28594 | GEO

Comprehensive analysis of metabolic and mitochondrial characteristics of extraembryonic endoderm cells

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

RNA-seq analysis of mESCs cultured on either Laminin-511 or gelatin coated dishes in either Std or 2i medium

Project description:Some mouse embryonic stem cell (mESC) lines need to be maintained on feeder cells in gelatin/Std condition. To eliminate the need for feeder cells, we decided to maintain the C57BL6/J mESCs on dishes coated with Laminin-511 (LN511) enabling maintenance of mESCs without feeder cells in Std condition (Domogatskaya et al., 2008). To compare the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on Laminin-511 coated dish, we performed RNA-Seq analysis. We found that the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on LN511 coated dish showed no considerable difference in expression patterns.

2020-06-04 | GSE132591 | GEO

Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

Project description:We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. iPSCs, NT-ESCs, and NT-iPSCs were exactly derived from the same MEF cells. The results indicate NT-ESCs give expression to the unique miRNAs other than both ESCs and iPSCs while pluripotent cells acquire or retain the pluripotent specific miRNAs compared with MEF. Furthermore, the comparison of different reprogramming cells suggests that several miRNAs have key roles in distinctly developmental potential reprogrammine cells. Small RNA profiles of MEF, ES, iPS, NT-ES and NT-iPS cells were generated by Solexa sequencing. MEF and ES cells were performed in triplicate. iPS, NT-ES and NT-iPS cells were sequenced in duplicate.

2014-07-05 | E-GEOD-52950 | biostudies-arrayexpress

The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors (SNEL iPSC and H2A.X deposition pattern)

Project description:Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4 and Myc (OSKM) into somatic cells. Though iPSCs are pluripotent, they frequently exhibit high variation in their quality as measured by chimera contribution and tetraploid (4n) complementation. Thus, improving the quality of iPSCs is an indispensable prerequisite for future iPSC-based therapy. Here we show that one major determinant for iPSCs quality is the selection of the reprogramming factors combination. Ectopic expression of Sall4, Nanog, Esrrb and Lin28 (SNEL) in MEFs efficiently generated high quality iPSCs as compared to other combinations of factors. SNEL-iPSCs produced approximately 5 times more efficiently “all-iPSC” mice compared to OSKM-iPSCs. While differentially methylated regions, transcript number of master regulators, establishment of ESC-specific super enhancers, and global aneuploidy were comparable between the lines, aberrant expression of 1,765 genes, trisomy of chromosome 8 and abnormal H2A.X deposition were frequently observed in poor quality OSKM-iPSCs. For high-quality iPSCs, H2A.X pattern of SNEL is most similar to that of ESC, OSK and OSKM have more devoid regions than SNEL iPSCs. Compare H2A.X deposition pattern of the OSKM 4-factor iPS cell lines (4N-), SNEL 4-factor iPS cell lines (4N+) with ChIP-Seq. The same background ES cell line as the control line.

2014-09-07 | E-GEOD-55731 | biostudies-arrayexpress

Netrin-1 facilitates somatic cell reprogramming by limiting Dcc pro-apoptotic activity.

Project description:The generation of induced pluripotent stem (iPS) cells holds great promise in regenerative medicine. However, the relative flaws in the understanding of the molecular mechanisms promoting or limiting reprogramming still hinder the efficient generation of high quality iPS cells. Whereas modulation of the initial Oct4, Sox2, Klf4 and c-Myc (OSKM) cocktail with new transcription factors has been extensively documented, comparatively little is known about soluble molecules promoting the process, even if such recombinant factors could be highly valuable for therapeutic applications. In this study we developed a large-scale identification method to uncover novel programmed cell death (PCD)-related mechanisms limiting somatic cell reprogramming to pluripotency (SCRP). We identified Netrin-1 and its dependence receptor Dcc (Deleted in Colorectal Carcinoma), previously described for their respective survival/death functions both in normal and oncogenic contexts, as novel key SCRP modulators. We show that the early phase of SCRP is accompanied with a strong Netrin-1 deficiency, due to the improper epigenetic regulation of the Ntn1 promoter by OSKM. Mechanistically, we demonstrate that such Netrin-1 imbalance induces apoptosis mediated by the dependence receptor Dcc in a p53-independent manner. Correction of the Netrin-1/Dcc equilibrium by gain-of-ligand and loss-of-receptor experiments constrains apoptosis and improves reprogramming. As a consequence, we propose a novel iPS derivation protocol including a sequential treatment with recombinant Netrin1 that greatly facilitates the generation of mouse and human iPS cells. RNA-sequencing of mouse embryonic fibroblasts (passage 2 and passage 4), mouse pre-iPS cells (passage 5 and passage 25), 1 clone of control iPS (passage 5 and passage 25) and 2 independent clones of "Netrin-1 derived" iPS cells (passage 5 and passage 25). For this analysis, mouse iPS cell lines were grown in KSR+LIF media.

2015-09-01 | E-GEOD-54107 | biostudies-arrayexpress

Effect of Aid deletion on the global gene expression iPS cells

Project description:It has been shown that DNA demethylation has a pivotal role in the generation of induced pluripotent stem (iPS) cells. However, the underlying mechanism is still unclear. Previous reports indicated that activation-induced cytidine deaminase (Aid) is involved in DNA demethylation in several developmental processes and cell fusion-mediated reprogramming. Based on the reports, we hypothesized that Aid may be involved in DNA demethylation during the iPS cell generation. In this study, we examined the function of Aid in iPS cell generation using Aid knockout (Aid-/-) mice expressing a GFP reporter under the control of a pluripotent stem cell marker, Nanog. By the introduction of Oct3/4, Sox2, Klf4 and c-Myc, Nanog-GFP positive iPS cells could be generated from the fibroblasts and primary B cells of Aid-/- mice. The Aid-/- iPS cells showed normal proliferation and gave rise to chimeras, indicating their capacity for self-renewal and pluripotency. Microarray analysis demonstrated that the global gene expression of Aid-/- iPS cells was similar to that of Aid+/+ iPS cells. Aid+/+ and Aid-/- iPS colonies were generated from Aid+/+ and Aid-/- MEFs and picked up mechanically. The clones were passaged four times on feeder cells and two times on gelatin-coated dishes to exclude the contamination of feeder cells. Subsequently, the RNA was isolated. Six Aid+/+ iPS cell clones and six Aid-/- iPS cell clones were compared by microarray. Samples from Aid+/+ and Aid-/-iPS cells

2014-04-10 | E-GEOD-51955 | biostudies-arrayexpress

PCGF6, a polycomb group protein, regulates mesodermal lineage differentiation in murine ES cells and functions in iPS reprogramming

Project description:Polycomb group (PcG) proteins comprise a large group of evolutionary conserved factors with essential roles for embryonic development and adult stem cell function. PcG proteins constitute two main multiprotein polycomb repressive complexes (PRC1 and PRC2) that operate in a hierarchical manner to silence gene expression. Functionally distinct PRC1 complexes are defined by Polycomb group RING finger protein (PCGF) paralogs. So far, six PCGF paralogs (PCGF1-6) have been identified but paralog-specific functions are not well understood. In our studies, we observed that Pcgf6 showed the highest expression level in undifferentiated murine embryonic stem cells (ESCs), blastocysts and testes. When ESCs differentiated, Pcgf6 expression strongly declined. To further investigate Pcgf6 biology, we established dox-inducible shRNA knockdown (KD) ESCs. Following Pcgf6 KD in ESCs the expression of pluripotency genes decreased, while mesodermal- and spermatogenesis-specific genes were de-repressed. Concomitantly with the elevated expression of mesodermal lineage markers, Pcgf6 KD ESCs showed increased hemangioblastic and hematopoietic activities. Finally, PCGF6 replaced SOX2 but not KLF4 or c-MYC in the generation of germline-competent iPS cells. Forced expression of Pcgf6 in OSKM-driven reprogramming increases iPS efficiency while Pcgf6 KD reduces the formation of ESC-like colonies. Together, these analyses show that Pcgf6 is non-redundantly involved in maintaining the pluripotent nature of ESCs and functions in iPS reprogramming. 6 samples were hybridized GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

2014-09-26 | E-GEOD-56126 | biostudies-arrayexpress

Global gene expression analysis in murine iPS cells derived with Nanog orthologs

Project description:This SuperSeries is composed of the following subset Series: GSE32464: Global gene expression analysis in murine iPS cells derived with mouse and human Nanog orthologs GSE32650: Global gene expression analysis in murine iPS cells derived with mouse, chick and zebrafish Nanog orthologs Refer to individual Series

2011-10-23 | E-GEOD-32715 | biostudies-arrayexpress

C/EBPα poises B cells for rapid reprogramming into iPS cells [ChIP-Seq]

Project description:C/EBPα induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem cells (iPSCs) when co-expressed with Oct4, Sox2, Klf4 and Myc (OSKM). However, how C/EBPα accomplishes these effects is unclear. We now found that transient C/EBPα expression followed by OSKM activation induces a 100 fold increase in iPSC reprogramming efficiency, involving 95% of the cells. During this conversion pluripotency and epithelial-mesenchymal transition genes become dramatically up-regulated and 60% of the cells express Oct4 within 2 days. C/EBPα acts as a pathbreaker since it transiently makes the chromatin of pluripotency genes more accessible to DNase I. It also induces the expression of the dioxygenase Tet2 and promotes its translocation to the nucleus where it binds to regulatory regions of pluripotency genes that become demethylated following OSKM induction. In line with these findings, overexpression of Tet2 enhances OSKM‐induced B cell reprogramming. Since the enzyme is also required for efficient C/EBPα-induced immune cell conversion, our data suggest that Tet2 provides a mechanistic link between iPSC reprogramming and B cell transdifferentiation. The rapid iPS reprogramming approach described should help to fully elucidate the process and has potential clinical applications. Change in Cebpa genome binding/occupancy, comparing primary B-cells treated with estradiol for 18h to induce C/EBPa to untreated cells.

2013-11-17 | E-GEOD-52373 | biostudies-arrayexpress

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