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SRP072989
Mus musculus
2 Downloadable Samples
Illumina HiSeq 4000
Description
Purpose:The goals of this study are to evaluate the effect of OX40 ligation on transcriptome profiling of in vitro polarized T helper 17 cell (RNA-seq). Methods: mRNA profiles of CD4+ T cells cultured in vitro under Th17-polarizing conditions for 48hrs (both Ctrl and OX40L treated groups) were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays Results: Among the 398 genes that were significantly affected by OX40, only about 11% were previously identified as ROR?t target genes in Th17 cells. Conclusions: Our study suggests that OX40 unlikely affects Th17 commitment, but most likely impairs their effector differentiation. As IL-17A and IL-17F are Th17-defining cytokines, their suppression suggests that OX40 may inhibits effector functions of Th17 cells. Overall design: mRNA profiles of CD4+ T cells cultured in vitro under Th17 differentiation conditions for 48 hours in the presence of WT-APCs or OX40L-TG APCs were generated by deep sequencing using Illumina RapidRun.
Publication Title
The Costimulatory Receptor OX40 Inhibits Interleukin-17 Expression through Activation of Repressive Chromatin Remodeling Pathways.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus, Homo sapiens
- 18 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We examined global gene expression patterns in response to PGC-1 expression in cells derived from liver or muscle.
Publication Title
Direct link between metabolic regulation and the heat-shock response through the transcriptional regulator PGC-1α.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Cell adhesion plays an important role in determining cell shape and function in a variety of physiological and pathophysiological conditions. While links between metabolism and cell adhesion were previously suggested, the exact context and molecular details of such a cross-talk remain incompletely understood.
Publication Title
Inhibition of Adhesion Molecule Gene Expression and Cell Adhesion by the Metabolic Regulator PGC-1α.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes and signal molecules. In this study we demonstrate, unexpectedly, that PGC-1, a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate expression of diverse genes encoding secreted molecules and extracellular matrix (ECM) components to modulate the secretome. We show that both endogenous and exogenous PGC-1 down-regulate expression of numerous genes encoding secreted molecules. Mechanistically, results obtained using mRNA stability measurements as well as intronic RNA expression analysis are consistent with a transcriptional effect of PGC-1 on expression of genes encoding secreted proteins. Interestingly, PGC-1 requires the central heat shock response regulator HSF1 to affect some of its targets, and both factors co-reside on several target genes encoding secreted molecules in cells. Finally, using a mass spectrometric analysis of secreted proteins, we demonstrate that PGC-1 modulates the secretome of mouse embryonic fibroblasts (MEFs).
Publication Title
Control of Secreted Protein Gene Expression and the Mammalian Secretome by the Metabolic Regulator PGC-1α.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 78 Downloadable Samples
- NextSeq 500
Description
Slow-cycling subpopulations exist in bacteria, yeast, and mammalian systems. In the case of cancer, slow-cycling subpopulations have been proposed to give rise to drug resistance. However, the origin of slow-cycling human cells is poorly studied, in large part due to lack of markers to identify these rare cells. Slow-cycling cells pass through a non-cycling period marked by low CDK2 activity and high p21 levels. Here, we use this knowledge to isolate these naturally slow-cycling cells from a heterogeneous population and perform RNA-sequencing to delineate the transcriptome underlying the slow-cycling state. We show that cellular stress responses – the p53 transcriptional response and the integrated stress response – are the most salient causes of spontaneous entry into the slow-cycling state. Overall design: mRNA profiling of spontaneously quiescent human cells and cells forced into quiescence by four different methods
Publication Title
Spontaneously slow-cycling subpopulations of human cells originate from activation of stress-response pathways.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq1500
Description
Human embryonic stem cells (hESCs) have the unique property of immortality, ability to infinitely self-renew and survive in vitro. In contrast to tumor-deribed cells, their immortality are free from any genomic abberations. Instead, they depend on the AKAP-Lbc/Rho signaling cascade. To understand the downstream way, we performed RNA-seq analyses between normal and AKAP-Lbc-depleted hESCs using the doxycyclin-inducible gene silensing strategy. Overall design: We use the genetically modified hESCs in which AKAP-13-targeting shRNA is induced by doxycyclin(dox) treatment. To minimize cell loss during treatment, anti-apoptotic factor Bcl-XL is overexpressed. We collected RNA from dox-treated and untreated cells in biological triplicate. We measured gene expression in these 2 sample groups using RNA-seq (illumina HiSeq) .
Publication Title
Rho-Signaling-Directed YAP/TAZ Activity Underlies the Long-Term Survival and Expansion of Human Embryonic Stem Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The transmission of information about the photic environment to the circadian clock involves a complex array of neurotransmitters, receptors, and second messenger systems. Using laser capture microscopy and microarray analysis, a population of genes rapidly induced by light in the suprachiasmatic nucleus is identified.
Publication Title
Identification of novel light-induced genes in the suprachiasmatic nucleus.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 4000
Description
Purpose: The objective of this study was to determine cardiac transcriptional pathways regulated in response to 1.) hypothyroidism and re-establishment of a euthyroid state and 2.) Med13-dependent cardiac transcriptional pathways regulated in response to hypothyroidism and re-establishment of a euthyroid state Overall design: Methods: WT and Med13 cardiac-specific knockout mice (Med13cKO) were put on a normal chow or PTU diet at 8 weeks of age for a duration of 4 weeks. A third group was put on a PTU diet for 4 weeks followed by 3 daily injections of T3.
Publication Title
Regulation of cardiac transcription by thyroid hormone and Med13.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 4000
Description
This is the first study to investigate mRNA expression profiling in regard to hepatic I/R and IPO by next-generation RNA-Seq. Our results may provide an experimental basis for elucidating the underlying mechanism of IPO and reveal candidate biomarkers with which to assess hepatic I/R injury Overall design: liver mRNA profiles of sham, I/R and IPO mice were generated by next-generation sequencing, in triplicate, using Illumina HiSeq 4000.
Publication Title
Gene Expression Profiling in Ischemic Postconditioning to Alleviate Mouse Liver Ischemia/Reperfusion Injury.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The rate of cell differentiation is tightly controlled and critical for normal development and stem cell differentiation. However, so far it has been difficult to control the rate of ESCs differentiation. Here we report the acceleration of the differentiation rate due to the activation of protein kinase A (PKA) and the associated early loss of embryonic stem cells (ESCs) pluripotency markers and the early appearance of mesodermal and other germ layer cell markers.
Publication Title
Protein kinase A accelerates the rate of early stage differentiation of pluripotent stem cells.
Sample Metadata Fields
Time
View Samples