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SRP043044
Escherichia coli
6 Downloadable Samples
Illumina HiSeq 2000
Description
Here we show using RNA-seq that cleavage by RNase E direct entry pervades in both the degradation and processing of RNA. We also give further evidence that direct entry is facilitated by cooperative interaction with segments in addition to the ones in which cleavage occurs. Overall design: RNA-seq profiles were compared between a temperature-sensitive mutant of rne and its congenic wild-type incubated at a non-permissive temperature. RNA seq profiles were also compared between samples before and after incubation with a 5''-sensing mutant of RNase E in vitro.
Publication Title
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.
Sample Metadata Fields
Cell line, Subject
View Samples- Rattus norvegicus
- 8 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
High dose level dibutyl phthalate (DBP) exposure of fetal rat testes in vivo inhibits testosterone production (i.e. endocrine disruption). Here, fetal testis mRNA levels were profiled following exposure to a DBP dose level that did not significantly reduce testosterone levels. The goal was to identify the constellation of gene expression changes that do not correlate with endocrine disruption.
Publication Title
Species-specific dibutyl phthalate fetal testis endocrine disruption correlates with inhibition of SREBP2-dependent gene expression pathways.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
In order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model. Overall design: Time series treatment of human A549 cells with dexamethasone or paired vehicle control.
Publication Title
Clustering gene expression time series data using an infinite Gaussian process mixture model.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Samples of primary tumors collected from 23 ovarian cancer patients
Publication Title
Machine learning predicts individual cancer patient responses to therapeutic drugs with high accuracy.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Leishmania major infected human dendritic cells (DCs) exhibit a marked induction of IL-12 ultimately promoting a robust Th1-mediated response associated with parasite killing and protective immunity. In this study, we utilized Affymetrix Genechips to globally assess the host cell genes and pathways associated with L. major infection during early infection (2, 4, 8, and 24 hrs) in human myeloid-derived DCs. Bioinformatic analyses of the hybridized microarray chips identified 728 genes, represented by 848 unique probe sets, which, when compared to uninfected samples were observed to be significantly differentially expressed by one-way ANOVA. Altogether, the data provide a genome-wide perspective on the transcriptional influences Leishmania species exert within human DCs during early infection, and provides a platform for further investigations toward functionally characterizing candidate genes of importance to the IL-12 based immune response to infections.
Publication Title
Human dendritic cells exhibit a pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in optic nerve (ON) gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.
Publication Title
Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in retina gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.
Publication Title
Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice.
Sample Metadata Fields
Specimen part, Time
View Samples- Saccharomyces cerevisiae
- 35 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation.
Publication Title
Cohesin proteins promote ribosomal RNA production and protein translation in yeast and human cells.
Sample Metadata Fields
Time
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To investigate the role of FoxO transcription factors as mediators of hematopoietic stem cell resistance to oxidative stress.
Publication Title
FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress.
Sample Metadata Fields
No sample metadata fields
View Samples