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Arabidopsis thaliana, Arabidopsis lyrata, Arabidopsis halleri
2 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana.
Publication Title
Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Apis mellifera
- 44 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 44 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
The objective of the study was to assess the technical error due to blending of individual samples into pools in experimental data.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Regulation of genes in shoots and roots and Arabidopsis in response to Zn-deficiency in wild-type and hma2 hma4 mutants plants
Publication Title
Systemic Upregulation of MTP2- and HMA2-Mediated Zn Partitioning to the Shoot Supplements Local Zn Deficiency Responses.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis) is one of the most critical in plant development. Here the newly identified mutant dez is photomorphogenic in the dark and is strongly enhanced in high Zn. dez displays a shortened hypocotyl, expanded cotyledons, an elongated root and differentiated plastids in the dark contrast to wild-type seedlings that are typically skotomorphogenic, with a long hypocotyl and unexpanded cotyledons protected by an apical hook, and undifferentiated etioplasts
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Pseudomonas aeruginosa
- 9 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
The transcriptome of two different Pseudomonas aeruginosa mutant strains were compared to the Pseudomonas aeruginosa wild type strain in the stationary growth phase
Publication Title
Function of the bacteriophytochrome BphP in the RpoS/Las-Quorum sensing network of Pseudomonas aeruginosa
Sample Metadata Fields
Subject, Time
View Samples
GSE5513- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Polyethylene glycol sorbitan monoacylates (Tween) are detergents of widespread use in plant sciences. We show them, notably Tween 20, to cause a rapid and complex change in transcript abundance which bears all characteristics of a PAMP / elicitor-induced defense response, and they do so at concentrations which cause no detectable deleterious effects on plant cellular integrity. The activity does not reside in the intact Tween molecule itself, but is caused by medium-chain fatty acids, notably lauric acid (LA), which are efficiently released from the Tween-backbone by the plant. The Tween / LA-response is independent of the jasmonate signalling system. Medium-chain fatty acids are thus novel elicitors/regulators of plant pathogen defense. The results also have several practical implications: (i) The use of Tweens and, as we show, several other detergents, as solvating/wetting agents on intact plants causes profound physiological changes which may mask actual effects of test compounds; (ii) Tweens by themselves can be regarded (and probably used) as economical, non-toxic, and safe-to-apply elicitors of inducible plant immunity against pathogens.
Publication Title
A novel regulatory system in plants involving medium-chain fatty acids.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 72 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A preliminary understanding of the phenotypic effect of copy number variation (CNV) of DNA segments is emerging. These rearrangements were demonstrated to influence, in a somewhat dose-dependent manner, the expression of genes mapping within. They were shown to also affect the expression of genes located on their flanks, sometimes at great distance. Here, we show by monitoring these effects at multiple life stages, that these controls over expression are effective throughout mouse development. Similarly, we observe that the more specific spatial expression patterns of CNV genes are maintained throughout life. However, we find that some brain-expressed genes appear to be under compensatory loops only at specific time-points, indicating that the influence of CNVs on these genes is modulated through development. We also observe that CNV genes are significantly enriched upon transcripts that show variable time-course of expression in different strains. Thus modifying the number of copy of a gene not only potentially alters its expression level, but possibly also its time of expression.
Publication Title
Copy number variation modifies expression time courses.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 61 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To study the effect of structural changes on expression, we assessed gene expression in genomic disorder mouse models. Both a microdeletion and its reciprocal microduplication mapping to mouse chromosome 11 (MMU11), which model the rearrangements present in Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes patients, respectively, have been engineered. We profiled the transcriptome of five different tissues affected in human patients in mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+) and uniallelic 2n (Deletion/Duplication) copies of the same region in an identical genetic background. The most differentially expressed transcripts between the four studied genotypes were ranked. A highly significant propensity, are mapping to the engineered SMS/PTLS interval in the different tissues. A statistically significant overrepresentation of the genes mapping to the flanks of the engineered interval was also found in the top-ranked differentially expressed genes. A phenomenon efficient across multiple cell lineages and that extends along the entire length of the chromosome, tens of megabases from the breakpoints. These long-range effects are unidirectional and uncoupled from the number of copies of the copy number variation (CNV) genes. Thus, our results suggest that the assortment of genes mapping to a chromosome is not random. They also indicate that a structural change at a given position of the human genome may cause the same perturbation in particular pathways regardless of gene dosage. An issue that should be considered in appreciating the contribution of this class of variation to phenotypic features.
Publication Title
Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 35 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Through post-transcriptional regulation of gene expression, miRNAs affect numerous regulatory pathways including those crucial for maintaining metabolic balance. Here we demonstrate that a neuronal-specific inhibition of miRNA maturation in adult mice leads to a rapid development of severe obesity, which is equally rapidly reversed. Development of obesity was associated with increased food intake and efficiency, and decreased locomotor activity. The ensuing decrease in body weight resembled a catabolic state with lowered O2-consumption and respiratory-exchange ratio. Brain transcriptome analyses in obese mice identified several obesity-related pathways including leptin, somatostatin, and nemo-like kinase signaling, as well as genes involved in feeding and appetite (e.g. Pmch, Neurotensin). A cluster of genes involved in synaptic plasticity was specifically enriched in post-obese mice that did not appear in obese mice. While other studies have identified a role for miRNAs in obesity our model is unique in that it allows for the study of processes involved in reversing obesity.
Publication Title
A neuron-specific deletion of the microRNA-processing enzyme DICER induces severe but transient obesity in mice.
Sample Metadata Fields
Specimen part, Time
View Samples