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SRP098927
Mus musculus
912 Downloadable Samples
Illumina HiSeq 2500
Description
Genetically engineered mouse models of cancer represent valuable biological tools that can be used to filter genome-wide expression datasets generated from human prostate tumours, and identify gene expression alterations that are functionally important to cancer development and progression. In this study, we have generated RNASeq data from tumours arising in two established mouse models of prostate cancer, PB-Cre/PtenloxP/loxP and p53loxP/loxPRbloxP/loxP, and integrated this with published human prostate cancer expression data to pinpoint cancer-associated gene expression changes that are conserved between the two species. In order to identify potential therapeutic targets, we then filtered this information for genes that are either known or predicted to be druggable. Using this approach, we identified the serine/threonine kinase MELK as a potential therapeutic target in prostate cancer. MELK was overexpressed in both human and murine prostate cancers, and high expression of MELK was associated with biochemical recurrence in prostate cancer patients. Overall design: 92 Samples
Publication Title
Identification of potential therapeutic targets in prostate cancer through a cross-species approach.
Sample Metadata Fields
Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 15 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants.
Publication Title
RNA polymerase II contributes to preventing transcription-mediated replication fork stalls.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 46 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Immunosenescence, the age-related decline in immune system function, is a general hallmark of aging. While much is known about the cellular and physiological changes that accompany immunosenescence, we know very little about the genetic influences on this phenomenon.
Publication Title
Age-specific variation in immune response in Drosophila melanogaster has a genetic basis.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Sexually dimorphic genome-wide binding of retinoid X receptor alpha (RXRα) determines male-female differences in the expression of hepatic lipid processing genes in mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Analysis of gender differential gene expression levels in mouse liver.
Publication Title
Sexually dimorphic genome-wide binding of retinoid X receptor alpha (RXRα) determines male-female differences in the expression of hepatic lipid processing genes in mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Vascular hypoperfusion is a pathological phenomenon in the glaucomatous optic nerve head. We report transcriptional responses in GFAP-negative LC cells exposed to in-vitro hypoxic stress (1%O2).
Publication Title
Hypoxia regulated gene transcription in human optic nerve lamina cribrosa cells in culture.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptional changes upon elicitor treatment over time (0, 30, 60 min) have been analysed with the A.thaliana Landsberg (wt) and fls2-17 (flagellin receptor mutant).
Publication Title
Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation.
Sample Metadata Fields
Age, Compound, Time
View Samples- Anopheles gambiae
- 4 Downloadable Samples
- Affymetrix Plasmodium/Anopheles Genome Array (plasmodiumanopheles)
Description
In the present study, we have investigated the effect of CpG Oligodeoxynucleotides (CpG-ODN) on the outcome of Plasmodium infection of the mosquito vectors Anopheles stephensi and Anopheles gambiae and on the modulation of mosquito immunity to Plasmodium. Anopheles mosquitoes inoculated with CpG-ODN showed significant reduction of Plasmodium infection rate and intensity. Microarrays were used to profile transcription of fat-body from CpG-ODN-treated mosquitoes. Mosquitoes were dissected 18h after ODN inoculation (immediately before feeding). Batches of 20 to 30 fat bodies (abdomen without midgut, ovaries and malpighian tubule]) were dissected in cold DEPC-treated phosphate-buffered saline (PBS) and processed for RNA preparation. Mosquitoes treated with CpG-ODNs are less susceptible to Plasmodium infection. Transcription profile of fat body indicates that protection was associated with coagulation/wound healing, while melanization appears to be depressed.
Publication Title
CpG-containing oligodeoxynucleotides increases resistance of Anopheles mosquitoes to Plasmodium infection.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 68 Downloadable Samples
- Illumina HiSeq 2500
Description
Rett syndrome (RTT) is a severe neurodevelopmental disorder that is caused by mutations in the gene methyl-CpG-binding-protein-2 (MECP2). However, the molecular mechanism by which these mutations mediate the RTT neuropathology remains enigmatic. In this study, we stimulated MeCP2-null cortical neurons (in vitro) and brains (in vivo) of a RTT mouse model to explore the effect of the loss of MeCP2 function on the activity-dependent transcriptomes of the cortex and hippocampus, respectively, using RNA-seq. These analyses revealed that the loss of MeCP2 results in aberrant global pattern of gene expression, characterized predominantly by higher levels of expression of activity-dependent genes, and anomalous alternative splicing events, specifically in response to neuronal activity. Overall design: For in vitro experiments, RNA-seq was performed on MeCP2-null (MT) and wild-type (WT) neuron-enriched cortical cultures that were either treated (T) with KCl for 3hr or not treated (N), after 10 days in culture. For in vivo experiments, RNA-seq was performed on hippocampi of MeCP2-null (MT) and wild-type (WT) mice that were either treated with kainic acid for 40 or 68 minutes, or not treated.
Publication Title
Activity-dependent aberrations in gene expression and alternative splicing in a mouse model of Rett syndrome.
Sample Metadata Fields
Specimen part, Treatment, Subject, Time
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- NextSeq 500
Description
Our analysis indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Overall design: Seven-day-old Arabidopsis wild-type (No-0) and 35S::KNAT1 seedlings growing in MS plates under continuous light were transferred to a liquid growing medium supplemented with 10 µM paclobutrazol (PAC) for 18 h. Seedlings were then incubated with 10 µM PAC+100 µM GA3 or maintained in 10 µM PAC for 5 h.
Publication Title
Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples