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GSE5301
Saccharomyces cerevisiae
18 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA.
Publication Title
The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
Illumina HiSeq 2000
Description
We report here mRNA-seq data of wild-type and Nat4-deletion mutant yeast cells. We also report mRNA-seq data of wild-type yeast cells grown under non-calorie restriction (NCR) and calorie restriction (CR) conditions. Overall design: Comparison of differential gene-expression changes detected in Nat4-deletion mutant and cells grown in calorie restriction
Publication Title
Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity.
Sample Metadata Fields
Cell line, Subject
View Samples- Caenorhabditis elegans
- 18 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
RNA Pol II accumulates at promoters of growth genes during developmental arrest.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 18 Downloadable Samples
Affymetrix C. elegans Genome Array (celegans)
Description
When C. elegans larvae hatch in the absence of food they persist in a stress resistant, developmentally arrested state (L1 arrest). We characterized mRNA expression genome-wide in a pair of bifurcating time series starting in the late embryo and proceeding through the hatch in the presence and absence of food (E. coli).
Publication Title
RNA Pol II accumulates at promoters of growth genes during developmental arrest.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 23 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Despite timely and successful surgery, 32% of patients with bilateral and 10% with unilateral cryptorchidism will develop azoospermia. Cryptorchid boys at risk of azoospermia display a typical testicular histology of impaired mini-puberty at the time of the orchidopexy.
Publication Title
Testicular gene expression in cryptorchid boys at risk of azoospermia.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Skeletal muscle senescence influences whole organism aging, yet little is known on the relay of pro-longevity signals from muscles to other tissues. We performed an RNAi screen in Drosophila for muscle-released cytokines (?myokines?) regulating lifespan and identified Myoglianin, the homolog of human Myostatin. Myoglianin is induced in skeletal muscles by the transcription factor Mnt and together they constitute an inter-organ signaling module that regulates lifespan, age-related muscle dysfunction, and protein synthesis across aging tissues. Both Mnt and Myoglianin activate already in young age the protective decline in protein synthesis that is typical of old age, while knock-down of Myoglianin impairs this process. Mechanistically, Mnt decreases the expression of nucleolar components in muscles while also decreasing nucleolar size in distant tissues via Myostatin/p38 MAPK signaling. Our results highlight a myokine-dependent inter-organ longevity pathway that coordinates nucleolar function and protein synthesis across aging tissues.
Publication Title
Intertissue control of the nucleolus via a myokine-dependent longevity pathway.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
We analyzed gene expression in human fibroblasts stimulated by platelet-derived growth factor-BB (PDGF-BB) or basic fibroblast growth factor (bFGF) for 1h and 24h. The results of two independent experiments were merged. SAM analysis identified 116 relevant probe sets. Hierarchical clustering of these probe sets showed divergent early gene regulation by PDGF and FGF but overlapping late response. We first analyzed genes commonly regulated by PDGF-BB and b-FGF more than 2 fold after 24h of stimulation and we found that these two growth factors repressed FOXO.
Publication Title
The transcription of FOXO genes is stimulated by FOXO3 and repressed by growth factors.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina Genome Analyzer
Description
This study set out to identify MLX transcriptional targets in muscle cells. C2C12 Myoblasts were virally transduced to increase MLX activity, by overexpression of the wild-type protein; and to decrease MLX activity by overexpression of a dominant negative MLX protein and by shRNA induced knockdown of MLX. Transcripts that were significantly and consistently regulated by the different modes of MLX modulation were identified. The largest proportion of these were genes encoding secreted proteins including growth factors, cytokines and extracellular proteins. We therefore conclude that MLX can regulate myokine transcripts. Overall design: mRNA profiles from C2C12 muscle cells with increased and decreased MLX activity were examined.
Publication Title
The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The Eol1 cell line has been derived from a patient with chronic eosiniphilic leukemia. Eol1 cells express the FIP1L1-PDGFRalpha oncogene. Inhibition of FIP1L1-PDGFRalpha with imatinib mesylate (Glivec) blocks proliferation and survival of the cells. We performed microarray expression analysis to identify genes specifically regulated by FIP1L1-PDGFRalpha using imatinib-treated cells as baseline. The list of regulated genes was consistent with the activation of STAT trancription factors by FIP1L1-PDGFRA.
Publication Title
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data.
Sample Metadata Fields
Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 26 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30C. Cells were washed with sterilized water the next day and re-suspended in SPII medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 to induce sporulation. Cells were sporulated at room temperature or 30C as indicated. Sporulation medium containing benomyl was always prepared freshly on the day of the experiment following the directions in {Shonn, 2000 #90}. Briefly, DMSO (dimethyl sulfoxide, Sigma-Aldrich) or benomyl [Methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, Sigma-Aldrich; 30 mg/ml stock in DMSO] was dissolved in near-boiling SPII medium to avoid precipitation. The medium was then allowed to slowly cool to 30C or room temperature. At the time of drug treatment, cells were filtered and immediately re-suspended in the medium containing benomyl or DMSO.
Publication Title
Novel response to microtubule perturbation in meiosis.
Sample Metadata Fields
No sample metadata fields
View Samples