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Arabidopsis thaliana
87 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 46 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.
Publication Title
Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Vitis vinifera
- 45 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Pierces disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierces disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis, and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlation of the classical concept of the disease triangle where environment impacts disease severity.
Publication Title
Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa.
Sample Metadata Fields
Age, Specimen part
View Samples- Citrus reticulata, Citrus x paradisi, Citrus sinensis, Citrus limon
- 17 Downloadable Samples
- Affymetrix Citrus Genome Array (citrus)
Description
To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon.
Publication Title
Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 42 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Macaca mulatta
- 33 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
Immunization of macaques with simian immunodeficiency virus with deletions in nef (SIVnef) has been shown to elicit protective immunity to infection by pathogenic SIV, yet our understanding of the mechanisms that orchestrate protection and prevent pathogenesis remains limited. In the study, we utilize whole-genome transcriptional profiling to reveal molecular signatures of protective immunity in circulating CD8+ T cells of rhesus macaques vaccinated with SIVmac239nef and challenged with pathogenic SIVmac251.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Macaca mulatta
- 32 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy.
Publication Title
Enhanced innate antiviral gene expression, IFN-α, and cytolytic responses are predictive of mucosal immune recovery during simian immunodeficiency virus infection.
Sample Metadata Fields
Specimen part
View Samples
GSE46356- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases.
Publication Title
Circadian clock regulates the host response to Salmonella.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mice lacking the beta 2 subunit (Chrnb2) of the neuronal nicotinic acetylcholine receptor display altered retinal waves and disorganized projections of the retinal ganglion cells to the lateral geniculate nucleus (LGN). mRNA populations from retinas and LGN from Chrnb2-/-and wild type (C57BL/6J) mice were compared at 4 days postnatal, when RGC segregation to the LGN begins in WT mice. Retinal mRNAs were also compared at adulthood.
Publication Title
Mouse mutants for the nicotinic acetylcholine receptor ß2 subunit display changes in cell adhesion and neurodegeneration response genes.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The deposit microarray data were generated in a study that comprehensively integrated gene expression profiles and metabolic responses of Caco-2 cells that incubated with either E. coli K-12 or O157:H7. The aim of this study is to examine the impact of colonic bacteria on the global gene expression regulation and metabolite levels of the host, and investigate the molecular mechanics of the E. coli/host interaction.
Publication Title
Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line.
Sample Metadata Fields
Cell line, Treatment
View Samples