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GSE6970
Mus musculus
16 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
Pressure overload (PO) leads first to cardiac hypertrophy and later to heart failure. In mice, PO leads to sex differences in cardiac morphology and function. However, early sex differences in gene regulation that precede sex differences in function have not yet been identified.
Publication Title
Sex-specific pathways in early cardiac response to pressure overload in mice.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
A mouse embryonic stem cell line was generated which stably expressed the ngn3 transcription factor under the control of the Tet-On inducible system using knock-ins in the ROSA26 and the HPRT loci. The undifferentiated mouse embryonic stem cells were then differentiated into Embryoid Bodies in suspension culture and were either treated with Doxycycline to induce NGN3 expression or left untreated as a contol. Cells were harvested at 12 hours, 24 hours and 48 hours.
Publication Title
A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation.
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment, Time
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Intrauterine growth restriction is a common complication of pregnancy. We induce IUGR in rats by bilateral uterine artery ligation at e18 of a 23 day gestation.
Publication Title
Neutralizing Th2 inflammation in neonatal islets prevents β-cell failure in adult IUGR rats.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 42 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 42 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells.
Publication Title
Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 38 Downloadable Samples
Illumina HiSeq 2000
Description
Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measured the gene expression dynamics of retinoic acid driven mESC differentiation using an unbiased single-cell transcriptomics approach. We found that the exit from pluripotency marks the start of a lineage bifurcation as well as a transient phase of susceptibility to lineage specifying signals. Our study revealed several transcriptional signatures of this phase, including a sharp increase of gene expression variability and a handover between two classes of transcription factors. In summary, we provide a comprehensive analysis of lineage commitment at the single cell level, a potential stepping stone to improved lineage control through timing of differentiation cues. Overall design: Bulk and single-cell RNA-seq (SCRB-seq and SMART-seq) of mouse embryonic stem cells after different periods of continuous exposure to retinoic acid. Bulk RNA-seq of cell lines derived after retinoic exposure and after differentiation with retinoic acid and MEK inhibitor combined.
Publication Title
Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells.
Sample Metadata Fields
Cell line, Subject
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Response to photoperiod in Arabidopsis wildtype, co, and ft mutant plants.
Publication Title
Integration of spatial and temporal information during floral induction in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets
Publication Title
SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 42 Downloadable Samples
- NextSeq500, IlluminaGenomeAnalyzerIIx
Description
The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. In the absence of degradation, the RNA polymerase II-associated factor (PAF) complex associates with MYC via interaction of its CDC73 subunit with a conserved domain in the amino-terminus of MYC ("MYC box I"), suggesting that a MYC/PAF complex is an intermediate in transcriptional activation. Since histone acetylation depends on a second highly conserved domain in MYCs amino-terminus ("MYC box II"), we propose that both domains co-operate to transfer elongation factors onto paused RNAPII. Overall design: RNA-Seq Experiments were performed in a primary breast epithelial cell line (IMEC).The cell line expressed doxycycline-inducible versions of MYC (WT;Kless,Swap=WTN-KC). Where indicated cells were transfected with siRNAs (siCtrl;siSKP2). Where indicated cells were treaed with the proteasome inhibitor MG132 or EtOH as solvent control. DGE was performed by comparing Dox-treated populations expressing either Dox-inducible MYC or a vector control or comparing Dox-induced cells with EtOH (solvent control) treated cells.
Publication Title
Ubiquitin-Dependent Turnover of MYC Antagonizes MYC/PAF1C Complex Accumulation to Drive Transcriptional Elongation.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 11 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Homeodomain (HD) proteins comprise a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, yet they paradoxically recognize very similar DNA sequences. To investigate how HDs control cell-specific gene expression patterns, we determined the DNA binding specificities of a broad range of HDs critical for Drosophila embryonic mesoderm development. These studies revealed particular sequences that are bound by one HD and not by others. Such HD-preferred binding sites are overrepresented in the noncoding regions of genes that are regulated by the corresponding HD. Moreover, we show at single-cell resolution in intact embryos that the HD Slouch (Slou) controls myoblast gene expression through unique DNA sequences that are preferentially bound by Slou. These findings demonstrate that the sequence of a HD-binding site dictates which HD family member binds to and regulates a particular enhancer. This represents a novel mechanism for how cell type-specific TFs induce the distinct genetic programs of individual embryonic cells.
Publication Title
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.
Sample Metadata Fields
Specimen part
View Samples