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SRP186637
Mus musculus
116 Downloadable Samples
Illumina HiSeq 2500
Description
We performed the circadian transcriptome analysis using the skeletal muscle from sedentary and exercised mice either in the early rest phase (ZT3) or in the early active phase (ZT15). By the combination with circadian transcriptomic and metabolomic analysis, we revealed time-of-day-dependent remodeling of circadian muscular metabolic pathways involved in glucose and glycerol metabolism after exercise. We found that only exercise in the early active phase elevates the levels of genes encoding glycolytic enzymes followed by the activation of fatty acid oxidation, branched-chain amino acid catabolism and ketogenesis/ketosis. This study demonstrates that time-of-day is a critical factor to modulate the impact of exercise on metabolic pathways within skeletal muscle. Overall design: Skeletal muscles from sedentary (sham-exercise) mice and mice subjected to acute treadmill exercise either in the early rest phase (ZT3) or in the early active phase (ZT15) were harvested after 0, 4, 8, 12, 16, and 20 hours after exercise or sham-exercise treatment.
Publication Title
Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis.
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Sequencing of 5'' ends of RNA molecules from control and exosome-depleted S2 cells. Overall design: CAGE library construction from RNA extracted from control and exosome-depleted cells.
Publication Title
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 21 Downloadable Samples
- Illumina HiSeq 1500
Description
Macrophages readily change their phenotype in response to exogenous stimuli. In this work, macrophages were stimulated under a variety of experimental conditions, and alterations in mRNA levels were analyzed. We identified three transcriptionally related populations of macrophages with immunoregulatory activity. They were generated by stimulating cells with TLR ligands, in the presence of three different “reprogramming” signals; high density immune complexes (IC), prostaglandin E2 (PGE2), or adenosine (Ado). All three of these cell populations produced higher levels of transcripts for IL-10, and growth and angiogenic factors. They also secreted reduced levels of inflammatory cytokines IL-1Beta, IL-6, and IL-12. All three macrophage phenotypes could partially rescue mice from lethal endotoxemia, and therefore we consider each to have immunoregulatory activity. This immunoregulatory activity occurred equally well in macrophages from stat6-deficient mice. The lack of STAT6 did not affect macrophages’ ability to reciprocally change cytokine production or to rescue mice from lethal endotoxemia. Furthermore, treatment of macrophages with IL-4 failed to induce similar phenotypic or transcriptional alterations. This work demonstrates that there are multiple ways to generate macrophages with immunoregulatory activity. These immunoregulatory macrophages are transcriptionally and functionally related, and quite distinct from macrophages treated with IL-4.
Publication Title
The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [AltAnalyz probeset-to-Ensembl mapping (huex10st)
Description
A growing body of evidence points to the essential role of bone marrow (BM) tumor microenvironment in Multiple Myeloma (MM) maintenance and progression. Mesenchymal stem cells (MSC) are one of the most important players in this scenario. Through direct and indirect interactions, these cells support MM cells by promoting increase of proliferation, migration, survival, and drug resistance. Additionally, an increasing number of evidence has been demonstrating that MSC from MM patients (MM-MSC) have several abnormalities when compared with their normal counterpart from normal donors (ND-MSC). Therefore, the aimed of our study was to explore the differences between MM-MSC and ND-MSC through gene expression analysis.
Publication Title
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Dengue viruses cause two severe diseases that alter vascular fluid barrier functions, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). While the mechanisms that lead to vascular permeability are unknown, the endothelium plays a central role in regulating fluid and cellular efflux from capillaries. Thus, dysregulation of endothelial cells functions by dengue virus infection may contribute to pathogenesis and severe disease.
Publication Title
Endothelial cells elicit immune-enhancing responses to dengue virus infection.
Sample Metadata Fields
Specimen part, Time
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We report RNA-seq data obtained from FACS-isolated live neurons at third instar larval or P14 pupal stage, and from BG3 cells. RNA from neurons with RNAi-based loss of shep or GFP control is used to construct stranded RNA-seq library. RNA from BG3 cells treated with dsRNA targeting shep or GFP is used to construct RNA-seq library. Overall design: RNA-seq data of loss-of-shep neurons and control neurons in larval and pupal stages, and from shep-depleted or control BG3 cells.
Publication Title
Shep regulates <i>Drosophila</i> neuronal remodeling by controlling transcription of its chromatin targets.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 16 Downloadable Samples
- Illumina Genome Analyzer II, Illumina HiSeq 2000
Description
Chromatin insulators are DNA-protein complexes situated throughout the genome capable of demarcating independent transcriptional domains. Previous studies point to an important role for RNA in gypsy chromatin insulator function in Drosophila; however, the identity of these putative insulator-associated RNAs is not currently known. Here we utilize RNA-immunoprecipitation and high throughput sequencing (RIP-seq) to isolate RNAs stably associated with gypsy insulator complexes. Strikingly, these RNAs correspond to specific sense-strand, spliced, and polyadenylated mRNAs, including two insulator protein transcripts. In order to assess the functional significance of these associated mRNAs independent of their coding function, we expressed untranslatable versions of these transcripts in developing flies and observed both alteration of insulator complex nuclear localization as well as improvement of enhancer-blocking activity. Together these data suggest a novel, noncoding mechanism by which certain mRNAs contribute to chromatin insulator function. Overall design: RIP-seq of insulator proteins with different library preparations and multiple biological replicates
Publication Title
Messenger RNA is a functional component of a chromatin insulator complex.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Human iPS cells derived from normal and Fragile-X fibroblasts in order to assess the capability of Fragile-X iPS cells to be used as a model for different aspects of Fragile-X syndrome. Microarry analysis used to compare global gene expression between human ES cells, the normal and the mutant iPS cells and the original fibroblasts, to demonstrate that the overall reprogramming process succeeded, and that the FX-iPS cells are fully reprogrammed cells.
Publication Title
Differential modeling of fragile X syndrome by human embryonic stem cells and induced pluripotent stem cells.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Caenorhabditis elegans
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
In this study, we analyzed the impact of a mutation in the wrn-1 gene compared to wild type worms and the dietary supplementation of vitamin C on the global mRNA expression of the whole C. elegans by the RNA-seq technology. Overall design: Whole C. elegans mRNA profiles at the L4 stage of wild type and wrn-1(gk99) mutant animals treated with or without 10 mM ascorbate were generated by deep sequencing, in triplicate, using the HiSeq 2000 machine form Illumina. Detailed statistics on the quality of the reads were calculated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The 50 base pairs raw sequences were aligned on the C. elegans ce10/W220 genome with TopHat using the Ensembl annotations provided with the Illumina iGenomes. The htseq-count software (http://www-huber.embl.de/users/anders/HTSeq) was used to count the number of reads aligned to each gene. These counts were then normalized relative to the sequencing depth with DESeq.
Publication Title
Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Carbonic anhydrase 1 (Car1), an early specific marker of the erythroid differentiation, has been used to distinguish fetal and adult erythroid cells since its production closely follows the - to -globin transition, but the molecular mechanism underlying transcriptional regulation of Car1 is unclear. Here, we show that Car1 mRNA decreases significantly when erythroid differentiation is induced in MEL cells. The Ldb1 protein complex including GATA1/SCL/LMO2 binds to the Car1 promoter in uninduced cells and reduced enrichment of the complex during differentiation correlates with loss of Car1 expression. Knockdown of Ldb1 results in a reduction of Ser2 phosphorylated RNA Pol II and Cdk9 at the Car1 promoter region, suggesting that Ldb1 is required for recruitment of Pol II as well as the transcription regulator P-TEFb to enhance elongation of Car1 transcripts. Taken together, these data show that Ldb1 forms a regulatory complex to maintain Car1 expression in erythroid cells.
Publication Title
Ldb1 regulates carbonic anhydrase 1 during erythroid differentiation.
Sample Metadata Fields
Specimen part
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