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SRP063667
Homo sapiens
10 Downloadable Samples
IlluminaGenomeAnalyzerII, IlluminaGenomeAnalyzer
Description
we treated Homo sapiens UMUC-3 cells with 5-AZA-CdR for 5, 9, 13 and 17 days and employed deep sequencing method to analyze alterations in gene expressions and alternative splicing
Publication Title
Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2'-deoxycytidine.
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 54 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Glucocorticoids (GCs) and protein kinase A (PKA)-activating agents (beta-adrenergic receptor agonists) are mainstream asthma therapies based on their ability to prevent or reverse excessive airway smooth muscle (ASM) constriction. Their abilities to regulate another important feature of asthma - excessive ASM growth are poorly understood. Recent studies have suggested that GCs render agents of inflammation such as interleukin 1beta and tumor necrosis factor alpha mitogenic to ASM, via suppression of (antimitogenic) induced cyclooxygenase-2-dependent PKA activity. To further explore the mechanistic basis of these observations, we assessed the effects of epidermal growth factor and interleukin 1beta stimulation, and the modulatory effects of GC treatment and PKA inhibition, on the ASM transcriptome by microarray analysis.
Publication Title
Glucocorticoid- and protein kinase A-dependent transcriptome regulation in airway smooth muscle.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 47 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Ethylene-dependent gene expression was assayed by treating with 1 uM ACC, an ethylene precursor, or a control treatment to Arabidopsis seedlings by transferring 6 day old Arabidopsis grown on a a nylon mesh to fresh ACC-containing or control media
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Arabidopsis thaliana
- 48 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Auxin-dependent transcript abundance was assayed by transferring 6 day old Arabidopsis grown on a a nylon mesh to IAA-containing or control media
Publication Title
A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Populus tremula x populus alba
- 11 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
Comparison of wild type Populus to transgenics expressing either a miRNA-resistant Populus ortholog of ATHB15/CORONA or miRNA-resistant Populus ortholog of REVOLUTA
Publication Title
The Populus class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plant volatiles can mediate plant-plant communication in the sense that plants attacked by herbivores can signal their unattacked neighbors of danger by emitting HIPVs. We call this the priming effect. Since the plant defense response is a systematic process involving numerous pathways and genes,to characterize the priming process, a time course study using a genome-wide microarray may provide more accurate information about the priming process. Furthermore, to what extent do the priming process and direct defense share similar gene expression profiles or pathways are also not clear.
Publication Title
Transcriptional analysis of Arabidopsis thaliana response to lima bean volatiles.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plants have developed a complicated resistance system, and they exhibit various defense patterns in response to different attackers. However, the determine factors of plant defense patterns are still not clear. Here, we hypothesized that damage patterns of plant attackers play an important role in determining the plant defense patterns. To test this hypothesis, we selected leafminer, which has a special feeding pattern more similar to pathogen damage than chewing insects, as our model insect, and Arabidopsis thaliana as the response plants. The local and systemic responses of Arabidopsis thaliana to leafminer feeding were investigated using the Affymetrix ATH1 genome array.
Publication Title
Transcriptome response analysis of Arabidopsis thaliana to leafminer (Liriomyza huidobrensis).
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples- Rattus norvegicus
- 129 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
Humans and ecological species have been found to have detectable body burdens of a number of perfluorinated alkyl acids (PFAA) including perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS). In mouse and rat liver these compounds elicit transcriptional and phenotypic effects similar to peroxisome proliferator chemicals (PPC) that work through the nuclear receptor peroxisome proliferator activated receptor alpha (PPARalpha). Recent studies indicate that along with PPARalpha other nuclear receptors are required for transcriptional changes in the mouse liver after PFOA exposure including the constitutive activated receptor (CAR) and pregnane X receptor (PXR) that regulate xenobiotic metabolizing enzymes (XME). To determine the potential role of CAR/PXR in mediating effects of PFAAs in rat liver, we performed a meta-analysis of transcript profiles from published studies in which rats were exposed to PFOA or PFOS. We compared the profiles to those produced by exposure to prototypical activators of CAR (Phenobarbital (PB)), PXR (pregnenolone 16 alpha-carbonitrile (PCN)), or PPARalpha (WY-14,643 (WY)). As expected, PFOA and PFOS elicited transcript profile signatures that included many known PPARalpha target genes. Numerous XME genes were also altered by PFOA and PFOS but not WY. These genes exhibited expression changes shared with PB or PCN. Reexamination of the transcript profiles from the livers of chicken or fish exposed to PFAAs indicated that PPARalpha, CAR, and PXR orthologs were not activated. Our results indicate that PFAAs under these experimental conditions activate PPARalpha, CAR, and PXR in rats but not chicken and fish. Lastly, we discuss evidence that human populations with greater CAR expression have lower body burdens of PFAAs.
Publication Title
Evidence for the involvement of xenobiotic-responsive nuclear receptors in transcriptional effects upon perfluoroalkyl acid exposure in diverse species.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 120 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Human Hepatocellular Carcinoma cells (HepG2) were exposed to six nanomaterials containing either Cerium oxide (CeO2) or Titanium oxide (TiO2) nanoparticles. Three different concentrations were tested: 0.3, 3, or 30 g/mL) for 3 days. Microarray analysis was performed to identify genes differentially expressed following exposure to these chemicals.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 34 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
In order to gain insight into the effects of aging on susceptibility to environmental toxins, we characterized the expression of xenobiotic metabolizing enzymes (XMEs) from the livers of male Brown Norway and F344 rats across the adult lifespan. To examine metabolic processes across lifespan after challenge with a xenobiotic compound, Brown Norway rats were exposed to 1.0 g/kg body weight toluene by oral gavage in corn oil (4ml/kg body weight) or corn oil alone.
Publication Title
Coordinated changes in xenobiotic metabolizing enzyme gene expression in aging male rats.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples