We have performed conditional inactivation of mef2c in the anterior heart field (AHF) of mice and observed a phenotypic spectrum of outflow tract anomalies in the conditional mutant hearts. In an effort to identify misregulated genes in the outflow tracts of the mutants, we have performed RNA-Seq on outflow tract samples dissected from E10.5 mutant and wild-type embryos. Overall design: There are four wild-type samples and four mutant samples.
MEF2C regulates outflow tract alignment and transcriptional control of Tdgf1.
No sample metadata fields
View SamplesGene expression profiling of supraclavicular brown, interscapular brown, inguinal white, and epididymal white adipose tissues from C57BL/6 male mice was performed by RNA-sequencing. Overall design: Total of 12 RNA samples (3 RNA samples from each adipose tissue type) from adipose tissues were used for RNA-sequencing analysis.
Identification and characterization of a supraclavicular brown adipose tissue in mice.
Sex, Specimen part, Cell line, Subject
View SamplesA pressing clinical challenge is identifying the etiologic basis of acute respiratory illness. Without reliable diagnostics, the uncertainty associated with this clinical entity leads to a significant, inappropriate use of antibacterials. Use of host peripheral blood gene expression data to classify individuals with bacterial infection, viral infection, or non-infection represents a complementary diagnostic approach.
Host gene expression classifiers diagnose acute respiratory illness etiology.
No sample metadata fields
View SamplesA 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.
A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation.
Sex, Specimen part, Cell line, Treatment, Time
View SamplesIntrauterine 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.
Neutralizing Th2 inflammation in neonatal islets prevents β-cell failure in adult IUGR rats.
Specimen part, Treatment
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.
Cell line
View SamplesKnowledge 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.
Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.
Cell line
View SamplesGene 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.
Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells.
Cell line, Subject
View SamplesResponse to photoperiod in Arabidopsis wildtype, co, and ft mutant plants.
Integration of spatial and temporal information during floral induction in Arabidopsis.
Specimen part
View SamplesESCs 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
SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.
No sample metadata fields
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