Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells (miRNA-Seq)

ABSTRACT: We performed an integrated analysis of RNA and proteins at the transition between naÃ¯ve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. We evaluated global miRNA profiles of embryonic stem cells cultured in either 10%FCS+LIF or 2i+LIF and of Epiblast-Like Aggregates derived from ES cells in 10%FCS+LIF or 2iL+LIF.

ORGANISM(S): Mus musculus

SUBMITTER: Luca Pandolfini

PROVIDER: E-GEOD-79654 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells (RIP)

Project description:We performed an integrated analysis of RNA and proteins at the transition between naÃ¯ve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. Cytoplasmic RNA-protein complexes from mouse embryonic stem cells at different stages of neural in vitro differentiation were immunoprecipitated with anti-Argonaute antibody and analyzed by microarray hybridization

2016-03-29 | E-GEOD-79649 | biostudies-arrayexpress

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells (RNAi)

Project description:We performed an integrated analysis of RNA and proteins at the transition between naÃ¯ve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. We assayed the impact of the functional inhibition of chromatin regulators on cell priming inhibiting chromatin remodeling activities by either pharmacological or genetic interference.

2016-03-29 | E-GEOD-79652 | biostudies-arrayexpress

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells (RNA)

Project description:We performed an integrated analysis of RNA and proteins at the transition between naÃ¯ve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. Comparison between EpiSC derived directly from mouse embryonic stem cells and from Epiblast-Like Aggregates

2016-03-29 | E-GEOD-79650 | biostudies-arrayexpress

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells (TRAP)

Project description:We performed an integrated analysis of RNA and proteins at the transition between naÃ¯ve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. We evaluated ribosome occupancy of mRNAs in embryonic stem cells and Epiblast-Like Aggregates by means of polysome profiling with a modified Translating Ribosome Affinity Purification protocol (TRAP).

2016-03-29 | E-GEOD-79653 | biostudies-arrayexpress

RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-29 | E-GEOD-79655 | biostudies-arrayexpress

Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells

Project description:We present a compendium DNA microarray analysis of multiple mouse ESCs and EGCs from different genetic backgrounds (strains 129 and C57BL/6) cultured under standard conditions and in differentiation-promoting conditions by the withdrawal of Leukemia Inhibitory Factor (LIF) or treatment with retinoic acid (RA). All pluripotent cell lines showed similar gene expression patterns, which separated them clearly from other tissue stem cells with lower developmental potency. Differences between pluripotent lines derived from different sources (ESC vs. EGC) were smaller than differences between lines derived from different mouse strains (129 vs. C57BL/6). Multiple ESC and EGC cell lines were cultured without feeders on gelatin coated, 6-well plates, 100,000 cells/well (10,000 cells/cm2) in 3 conditions: 1) in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol, and penicillin/streptomycin (50U/50ug per ml); 2) in ES medium without LIF; 3) in complete ES medium plus 1 uM RA. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added, RNA extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in DEPC dH2O.

2010-06-11 | E-GEOD-5914 | biostudies-arrayexpress

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 (RNA-Seq data)

Project description:We report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to chromosomal regions bound by CTCF and cohesin. Enrichment for TAF3/CTCF/cohesin bound regions distinguishes TAF3-activated from TAF3-repressed genes. Our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions to safeguard the finely-balanced transcriptional programs that give rise to pluripotency. Comparison of genome-wide expression patterns between TAF3-knockdown and WT embryonic stem cells using mRNA-Seq. Significantly differentially expressed protein-coding genes were identified by comparing control and knock-down samples at each timepoint (ES, embryoid body day 3 (EB3), EB6). Single and paired-end samples were combined at each timepoint, resulting in 3 tests for each gene (based on 8, 4, 4 independent measurements at ES ,EB3, EB6, respectively).

2011-09-02 | E-GEOD-31271 | biostudies-arrayexpress

Transcriptome of ESCs, EpiSCs and reverted ES by MM401 (Mll1 inhibitor)

Project description:This study describes the transcriptome profiling of: 1) mouse ES cells and EpiSCs in LIF/serum-free (KSR) medium; 2) E14Tg2a (E14) ES cells in LIF/Serum with or without MM401 treatment; 3) rES reverted form EpiSC by MM401/LIF KSR treatment at P6, P30. RNA-Seq profiling on mouse pluripotent cells. Biological duplicates of each sample are labled as rep1/2.

2016-02-19 | E-GEOD-66110 | biostudies-arrayexpress

Gene expression data from mouse ES cell-derived primitive NSCs and definitive NSCs

Project description:Primitive neural stem cells (NSCs) could be derived from pluripotent mouse embryonic stem (ES) cells, and then differentiate into definitive-type neural stem cells which resemble NSCs obtained from the central nervous system. Hence, primitive NSCs define an early stage of neural induction and provide a model to understand the mechanism that controls initial neural commitment. In this study, we performed microarray assay to analyze the global transcriptional profiles in mouse ES cell-derived primitive and definitive NSCs and to depict the molecular changes during the multi-staged neural differentiation process. Primitive NSCs derived directly from ESCs in Lif (p-NSC_L), primitive NSCs that were sub-cultured in the presence of Lif and FGF (p-NSC_LF), as well as definitive NSCs derived from primitive NSCs in medium containing FGF and EGF, were collected for RNA extraction and hybridization on Affymetrix microarrays. Mouse ESCs and NSCs obtained from mouse embryonic brain (E11.5) were included for controls. For each cell type, we collected two biological replicate samples for microarray analysis.

2014-03-01 | E-GEOD-44608 | biostudies-arrayexpress

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

Project description:We report that ES cells cultured in ground state (2i and 2i/LIF) culture conditions are heterogeneous and show heterogeneus expression of extraembryonic markers. Using a highly sensitive reporter for the endoderm marker Hex we can sort Hex high and low populations from either serum/LIF or 2i/LIF and demonstrate that they have different functional properties. Here we explored the transcriptional basis of these functional differences and noted that Hex low (HV-) and Hex high (HV+) populations showed more distinct expression profiles in 2i/LIF than in serum/LIF. Additionally in 2i/LIF the HV+ population showed an upregulation of extraembryonic markers (such as trophoblast stem cell specific genes) and also imprinted genes compared to the HV- population, which is not observed when these populations are sorted from serum/LIF. We also analysed the transcriptional effect of LIF in 2i by analysing unsorted ES cells cultured in either 2i alone or 2i with LIF. We observed that the addition of LIF led to an upregulation of extraembryonic markers but did not effect the expression of pluripotency genes, other than Klf4. Additionally, the most significantly upregulated genes from 2i/LIF cultured ES cells compared to 2i cultured ES cells showed the greatest correlation to placental tissue when compared to the GNF tissue specific expression database. This analysis, alongside functional experiments, suggested that HV+ ES cells in 2i/LIF corresponded to an extraembryonically primed population of cells and that the addition of LIF supported this population. RNA-seq of sorted Hex low and high expressing ES cell populations cultured in serum/LIF or 2i/LIF as well as unsorted ES cells from 2i or 2i/LIF.

2013-06-11 | E-GEOD-45182 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data