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SRP009043
Saccharomyces cerevisiae
22 Downloadable Samples
Illumina Genome Analyzer II
Description
We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Overall design: Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.
Publication Title
Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Aeromonas caviae has been associated with human gastrointestinal disease. Strains of this species typically lack virulence factors (VFs) such as enterotoxins and hemolysins that are produced by other human pathogens of the Aeromonas genus. Microarray profiling of murine small intestinal extracts, 24 hours after oral infection with an A. caviae strain, provides evidence of a Th1 type immune response. A large number of gamma-interferon (-IFN) induced genes are up-regulated as well as several tumor necrosis factor-alpha (TNF-) transcripts. A. caviae has always been considered an opportunistic pathogen because it lacks obvious virulence factors. This current effort suggests A. caviae colonizes murine intestinal tract and causes what has been described by others as a dysregulatory cytokine response leading to an irritable bowel-like syndrome. This response would explain why a number of diarrheal waterborne outbreaks have been attributed to A. caviae even though it lacks obvious enteropathogenic properties.
Publication Title
Aeromonas caviae strain induces Th1 cytokine response in mouse intestinal tract.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
How secondary CD4 T cell effectors, derived from resting memory cells, differ from primary cells, derived from nave precursors, and how such differences impact recall responses to pathogens is unknown.
Publication Title
Memory CD4+ T-cell-mediated protection depends on secondary effectors that are distinct from and superior to primary effectors.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 268 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Aims: To assess the virulence of multiple Aeromonas spp. using two models, a neonatal mouse assay and a mouse intestinal cell culture.
Publication Title
Evaluating virulence of waterborne and clinical Aeromonas isolates using gene expression and mortality in neonatal mice followed by assessing cell culture's ability to predict virulence based on transcriptional response.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
How IL-2 produced by secondary CD4 T cell effectors, derived from resting memory cells, impacts memory CD4 T cell function and survival to memory following antigen re-encounter is unknown.
Publication Title
Effector CD4 T-cell transition to memory requires late cognate interactions that induce autocrine IL-2.
Sample Metadata Fields
Treatment, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Ctla4-/- mice suffer from a severe autoimmunity characterized by indiscriminate self-reactive T cell activation. Itk-/-Ctla4-/- (DKO) mice are protected from lethal autoimmunity despite a fulminant autoimmune process in the LNs as self-reative T cells fail to migrate to destroy tissues.
Publication Title
CD28 and ITK signals regulate autoreactive T cell trafficking.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
RhoBTB2 is a novel Rho GTPase that undergoes loss, underexpression and mutation in breast and lung cancer. We have shown that we can mimic loss of RhoBTB2 through siRNA treatment of primary cells. We propose to perform comparative microarray analysis of primary lung cells to establish the identification of the gene targets of RhoBTb2 regulation.
Publication Title
The atypical Rho GTPase RhoBTB2 is required for expression of the chemokine CXCL14 in normal and cancerous epithelial cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 21 Downloadable Samples
- Illumina HiSeq 2000
Description
To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory. Overall design: Drosophila trained with an appetitive conditioning paradigm using Sucrose were collected prior to starvation, training, and 1 or 4 hours post-training, 5 to 6 replicates each, for RNA-Seq analysis of the fly heads with an Illumina HiSeq 2000.
Publication Title
Antimicrobial peptides modulate long-term memory.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Genome-wide profiling establishes that human cytomegalovirus (HCMV) exerts an extensive, unforeseen level of specific control over which cellular mRNAs are recruited to or excluded from polyribosomes.
Publication Title
Global reprogramming of the cellular translational landscape facilitates cytomegalovirus replication.
Sample Metadata Fields
Specimen part, Disease, Treatment
View Samples- Equus caballus
- 9 Downloadable Samples
- Equus caballus Gene 1.0 ST Array (equgene10st)
Description
Electroacupuncture is the combination of traditional acupuncture and modern electrotherapy. Here we provide a mechanism for the beneficial effects of electroacupuncture and show that stimulation of the equine acupoints LI-4, LI-11 and GV-14 and Bai-hui results in mobilization of mesenchymal stem cells (MSCs) into the systemic circulation, which was accompanied by a time-dependent increase in plasma levels of norepinephrine (p=0.02). MSC differentiation was preferentially directed towards osteogenic rather than adipogenic lineages. Additionally, MSCs enhanced arterialization of blood vessels in vivo when implanted with human endothelial colony forming cells in oligomeric collagen matrices in NOD/SCID mice. When compared to equine bone marrow-derived MSCs or to equine adipose-tissue-derived MSCs, through the use of a microarray, these cells clustered separately. The electroacupuncture -mobilized cells showed increased expression of genes involved in cell growth and proliferation, compared to the bone marrow cells. These findings provide a new insight into the mechanism of the beneficial effects of acupuncture. Our findings suggest the involvement of neuronal regulation in the mobilization of reparative MSCs, and use of electroacupuncture at these designated points may be considered to treat acute and chronic inflammation following injury for which MSCs have been deemed beneficial.
Publication Title
Electroacupuncture Promotes Central Nervous System-Dependent Release of Mesenchymal Stem Cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples