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GSE29303
Populus trichocarpa
48 Downloadable Samples
Affymetrix Poplar Genome Array (poplar)
Description
Previous research has shown that glutamine and sucrose treatment of excised poplar stems induces bark storage protein (BSP) gene expression. The objective of this research is to identify changes in gene expression associated with metabolic regulation of nitrogen storage and cycling and use this information to identify potential regulatory genes. Significant, differentially expressed genes were identified in excised poplar stems incubated in solutions of glutamine, sucrose, glycine, glutamine+glucose, and glutamine+sucrose compared to incubation in a water control.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Populus trichocarpa
- 21 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
The role of bark storage proteins (BSPs) in seasonal N storage and cycling has been well documented. However, the regulatory mechanisms and pathways associated with this physiological process are poorly understood. The objective of this study is to investigate global patterns of gene expression associated with photoperiod regulated BSP accumulation and to identify candidate genes, pathways and regulatory factors governing N storage and cycling in poplar. In this study, differential expression of protease inhibitors, proteases, transcription factors, and other genes coincided with increased BSP gene expression, suggesting a complex regulatory network that might play an important role in BSP accumulation.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Populus trichocarpa
- 12 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
Seasonal nitrogen (N) storage and reuse is important to the N-use efficiency of temperate deciduous trees. In poplar, bark storage proteins (BSPs) accumulate in protein storage vacuoles of the bark parenchyma and xylem ray cells in the fall. During spring growth, N from stored BSPs is remobilized and utilized by growing shoots. The goal of this study is to investigate global gene expression changes in the bark during BSP remobilization and shoot regrowth under long-day conditions.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Vascular disrupting agents (VDA) represent a novel approach to the treatment of cancer, resulting in collapse of tumor vasculature and tumor death. 5,6-Dimethylxanthenone-4-acetic acid (DMXAA) is a VDA currently in advanced Phase II clinical trials, yet its precise mechanism of action is unknown despite extensive preclinical and clinical investigations. The data presented herein demonstrate that DMXAA is a novel and specific activator of the TBK1-IRF-3 signaling pathway. DMXAA treatment of primary murine macrophages resulted in robust IRF-3 activation, a ~750-fold increase in IFN-beta mRNA and, in contrast to the potent Toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS), signaling was independent of mitogen-activated protein kinase (MAPK) activation and elicited minimal NF-kappaB-dependent gene expression. DMXAA-induced signaling was critically dependent on the IRF-3 kinase, TBK1, and IRF-3, but MyD88-, TRIF-, IPS-1/MAVS-, and IKKbeta-independent, thus excluding all known TLRs and cytosolic helicase receptors. DMXAA pretreatment of murine macrophages induced a state of tolerance to LPS and vice versa. In contrast to LPS stimulation, DMXAA-induced IRF-3 dimerization and IFN-beta expression were inhibited by salicylic acid (SA). These findings detail a novel pathway for TBK-1-mediated IRF-3 activation and provide new insights into the mechanism of this new class of chemotherapeutic drugs.
Publication Title
The chemotherapeutic agent DMXAA potently and specifically activates the TBK1-IRF-3 signaling axis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 34 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Exon usage analysis in in vitro cultured fibroblast cells. To assay the genome-wide splicing changes during cellular senescence, we performed splicing analysis on young and old normal fibroblasts, and in fibroblasts +/- tert (telomerase protein subunit Tert immortalized).
Publication Title
Progerin and telomere dysfunction collaborate to trigger cellular senescence in normal human fibroblasts.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Intrinsic variations in the development of lung injury among patients undergoing radiotherapy for tumors in the thoracic region suggest there are one or more genes that influence the development and severity of radiation pneumonitis and/or fibrosis.
Publication Title
Pathophysiological mechanisms underlying phenotypic differences in pulmonary radioresponse.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
micrarray profiling on Arabidopsis thaliana col-0, cry1 and hfr1 in response to dark and 1 h blue light treatment
Publication Title
HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos but mutations result in a pair-rule phenotype. Previously characterized Ftz-F1 target genes were co-regulated by Ftz, which is expressed in stripes, consistent with the pair-rule phenotype observed for ftz-f1 and ftz mutants. However, attempts to identify new target genes on the basis of Ftz-F1 and Ftz binding sites alone has met with only limited success. To discern the rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos.
Publication Title
Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers.
Sample Metadata Fields
Specimen part
View Samples- Macaca mulatta
- 12 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Impact of moderate calorie restriction on the reproductive neuroendocrine axis of male rhesus macaques
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a novel calcium-binding protein and used the Affymetrix whole-genome arrays to define downstream targets of this important protein.
Publication Title
A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis.
Sample Metadata Fields
Specimen part, Treatment
View Samples