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GSE14739
Sus scrofa
80 Downloadable Samples
Affymetrix Porcine Genome Array (porcine)
Description
Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material.
Publication Title
Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis.
Sample Metadata Fields
Sex, Specimen part
View Samples- Sus scrofa
- 63 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues.
Publication Title
Transcriptome architecture across tissues in the pig.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of the study was to evaluate cocaine-induced changes in gene expression in a dopaminergic model.
Publication Title
Transcriptomic and genetic studies identify NFAT5 as a candidate gene for cocaine dependence.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cyclin-dependent kinases (CDK) are rational cancer therapeutic targets fraught with the development of acquired resistance by tumor cells. Through integrated fluxomics and transcriptomics approaches, we show that the inhibition of CDK4/6 causes enhanced metabolism of glucose, glutamine and amino acids, a metabolic reprogramming directed by the MYC transcription factor. Upon inhibition of CDK4/6, MYC is stabilized and its accumulation induces an upregulation of the mTOR pathway and increased glutamine metabolism and production of -ketoglutarate, a prolyl hydroxylase substrate that triggers HIF1 hydroxylation and degradation. These MYC-driven adaptations to CDK4/6 inhibition render cells highly sensitive to inhibitors of mTOR and glutaminase and to hypoxia, revealing that drug resistance can mechanistically promote the emergence of new vulnerabilities that can be exploited therapeutically.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 5 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Composts are the products obtained after the aerobic degradation of different types of organic matter wastes and can be used as substrates or substrate/soil amendments. There are a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost as growing medium compared to standard substrates. The purpose of this study was to unravel the gene expression alteration produced by the compost to gain knowledge about the mechanisms involved in the compost-induced systemic resistance.
Publication Title
Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
LRRK2 mutations are the most common genetic cause of Parkinsons disease (PD). We performed a whole-genome RNA profiling of putamen tissue from idiopathic PD (IPD), LRRK2-associated PD (G2019S mutation), neurologically healthy controls and one asymptomatic LRRK2 mutation carrier, by using the Genechip Human Exon 1.0-ST Array. The differentially expressed genes found in IPD revealed an alteration of biological pathways related to long term potentiation (LTP), GABA receptor signalling, and calcium signalling pathways, among others. These pathways are mainly related with cell signalling cascades and synaptic plasticity processes. They were also altered in the asymptomatic LRRK2 mutation carrier but not in the LRRK2-associated PD group. The expression changes seen in IPD might be attributed to an adaptive consequence of a dysfunction in the dopamine transmission. The lack of these altered molecular pathways in LRRK2-associated PD patients suggests that these cases could show a different molecular response to dopamine transmission impairment.
Publication Title
Microarray expression analysis in idiopathic and LRRK2-associated Parkinson's disease.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
LRRK2 mutations are the most common genetic cause of Parkinsons disease (PD). We performed a whole-genome RNA profiling of locus coeruleus post-mortem tissue from idiopathic PD (IPD) and LRRK2-associated PD patients. The differentially expressed genes found in IPD and LRRK2-associated PD were involved in the gene ontology terms of synaptic transmission and neuron projection. In addition, in the IPD group we found associated genes belonging to the immune system. Pathway analysis of the differentially expressed genes in IPD was related with neuroactive-ligand receptor interaction and with immune system pathways. Specifically, the analysis highlighted differential expression of genes located in the chromosome 6p21.3 belonging to the class II HLA. Our findings support the hypothesis of a potential role of neuroinflammation and the involvement of the HLA genetic area in IPD pathogenesis. Future studies are necessary to shed light on the relation of immune system related pathways in the etiopathogenesis of PD.
Publication Title
Brain transcriptomic profiling in idiopathic and LRRK2-associated Parkinson's disease.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Mus musculus
- 1 Downloadable Sample
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Many concurrent arrays were run for different projects. All test conditions were tested in all animal models. Animal models were (i) healthy CD1 mice (abbreviation CN), or (ii) STZ-induced diabetic CD1 littermates (STZ). Treatment conditions were (i) untreated animals (no prefix), (ii) treatment with 30ul saline and electrotransfer ("e" prefix), (iii) treatment with 75ug noncoding parental plasmid pGG2-CMV ("p" prefix), or (iv) treatment with 37.5ug each (75ug net) of pGG2-CMV-hIns and pGG2-CMV-rGck expressing human insulin and rat glucokinase respectively ("t" prefix). All samples were harvested 7 days after treatment.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject, Compound, Time
View Samples- Saccharomyces cerevisiae
- 8 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We determined and classified Yak1-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of different haploid MATa yeast strains of the following genotypes:YAK1 (468=YHUM0468), yak1 (1313=YHUM1313), strain YHUM1313 (yak1) carrying a high copy plasmid with YAK1 (1313Yhc) and strain YHUM1313 (yak1) carrying a high copy plasmid with YAK1 K398R (1313KDhc). All strains were grown in duplicate in YNB medium supplemented with tryptophan at 30 degrees Celsius to an optical density of 1.0 before extraction of total RNA and transcriptional profiling.
Publication Title
No associated publication
Sample Metadata Fields
Sex
View Samples- Saccharomyces cerevisiae
- 4 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We determined and classified Whi3-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of two different haploid MATa yeast strains of the following genotypes: WHI3 strain (468=YHUM0468) and whi3 strain (1105=YHUM1105).Both starins were grown in duplicate in YNB medium with tryptophan at 30°C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling
Publication Title
No associated publication
Sample Metadata Fields
Sex
View Samples