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GSE14420
Arabidopsis thaliana
17 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between Arabidopsis lines with altered expression of ANAC102 (over-expressed and knocked-out) and wild-type. ANAC102 is a putative NAC domain transcription factor. Gene expression was compared between an ANAC102 over-expressing line and parental ecotype C24 under ambient atmosphere to determine which genes ANAC102 is capable of regulating. Gene expression was also compared between three week old plants of an ANAC102 knock-out line and parental ecotype Col-0 under 0.1% Oxygen and ambient atmosphere conditions to determine which genes may require ANAC102 for appropriate expression under these conditions. Gene expression was also compared between imbibed seeds of an ANAC102 knock-out line and parental ecotype Col-0 following a 0.1% Oxygen treatment.
Publication Title
The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment.
Sample Metadata Fields
No sample metadata fields
View Samples- Gossypium hirsutum
- 8 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants.
Publication Title
Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.).
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between root RNA samples from three-week-old Arabidopsis Col-0 plants subjected to 0.1% oxygen (balance nitrogen) or ambient atmospheric conditions.
Publication Title
Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana x arabidopsis lyrata, Arabidopsis lyrata subsp. lyrata, Arabidopsis thaliana x arabidopsis halleri subsp. gemmifera, Arabidopsis thaliana, Arabidopsis halleri subsp. gemmifera
- 2 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines.
Publication Title
Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We compared the expression among three lines, Col, C24, and their hybrids at 10 days after sowing (DAS).
Publication Title
Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 24 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Cobalt is a transition group metal present in trace amounts in the human diet, but in larger doses it can be acutely toxic or cause adverse health effects in chronic, long term exposures. Its use in many industrial processes and alloys worldwide presents opportunities for occupational exposures, as well as exposures to military personnel. While the toxic effects of cobalt have been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify potential biomarkers of exposure or effect, we exposed two rat liver-derived cell lines, H4-II-E-C3 and MH1C1, to two concentrations of cobalt chloride. We examined changes in gene expression using DNA microarrays in both cell lines and examined changes in cytoplasmic protein abundance in MH1C1 cells using mass spectrometry. We chose to closely examine differentially expressed genes and proteins changing in abundance in both cells lines in order to remove cell line specific effects. We identified enriched pathways, networks, and biological functions using commercial bioinformatic tools and manual annotation. Many of the genes, proteins, and pathways modulated by exposure to cobalt appear to be due to an induction of a hypoxic-like response and oxidative stress. Genes that may be differentially expressed due to a hypoxic-like response are involved in Hif-1 signaling, glycolysis, gluconeogenesis, and other energy metabolism related processes. Gene expression changes linked to oxidative stress are also known to be involved in the NRF2-mediated response, protein degradation, and glutathione production. Using microarray and mass spectrometry analysis, we were able to identify modulated genes and proteins, further elucidate the mechanisms of toxicity of cobalt, and identify biomarkers of exposure and effect in vitro, providing targets for focused in vitro studies.
Publication Title
Exposure to cobalt causes transcriptomic and proteomic changes in two rat liver derived cell lines.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
Illumina Genome Analyzer
Description
Low-oxygen stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from low-oxygen stressed and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from 3 families. Low-oxygen stress resulted in changes to the abundance of 46 miRNAs from 19 families, and all 3 tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the low-oxygen responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to low oxygen, and that a major signal for these responses is likely to be dependent on mitochondrial function. Keywords: Small RNA transcriptome analysis Overall design: Examination of root tissue under 2 different environments, control and low oxygen
Publication Title
Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis.
Sample Metadata Fields
Age, Subject
View Samples- Hordeum vulgare
- 6 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Comparison of wild type barley plants versus plants over-expressing ODDSOC2; a vernalization responsive MADS box gene ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aaron Greenup. The equivalent experiment is BB93 at PLEXdb.]
Publication Title
ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 59 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
U.S. Service Members and civilians are at risk of exposure to a variety of environmental health hazards throughout their normal duty activities and in industrial occupations. Metals are widely used in large quantities in a number of industrial processes and are a common environmental toxicant, which increases the possibility of being exposed at toxic levels. While metal toxicity has been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify candidate biomarkers, rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2 and Na2Cr2O7, with livers harvested at 1, 3, or 7 days after exposure. Cd and Cr accumulated in the liver at 1 day post exposure. Cd levels remained elevated over the length of the experiment, while Cr levels declined. Metal exposures induced ROS, including hydroxyl radical (OH), resulting in DNA strand breaks and lipid peroxidation. Interestingly, ROS and cellular damage appeared to increase with time post-exposure in both metals, despite declines in Cr levels. Differentially expressed genes were identified via microarray analysis. Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers.
Publication Title
Temporal changes in rat liver gene expression after acute cadmium and chromium exposure.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
MicroRNAs (miRNAs) post-transcriptionally regulate the expression of thousands of distinct mRNAs. While some regulatory interactions help to maintain basal cellular functions, others are likely relevant in more specific settings, such as response to stress. Here we describe such a role for the mir-290-295 cluster, the dominant miRNA cluster in mouse embryonic stem cells (mESCs). Examination of a target list generated from bioinformatic prediction, as well as expression data following miRNA loss, revealed strong enrichment for apoptotic regulators, two of which we validated directly: Caspase 2, the most highly conserved mammalian caspase, and Ei24, a p53 transcriptional target. Consistent with these predictions, mESCs lacking miRNAs were more likely to initiate apoptosis following genotoxic exposure to gamma irradiation or doxorubicin. Knockdown of either candidate partially rescued this pro-apoptotic phenotype, as did transfection of members of the mir-290-295 cluster. These findings were recapitulated in a specific mir-290-295 deletion line, confirming that they reflect miRNA functions at physiological levels. In contrast to the basal regulatory roles previously identified, the pro-survival phenotype shown here may be most relevant to stressful gestations, where pro-oxidant metabolic states induce DNA damage. Similarly, this cluster may mediate chemotherapeutic resistance in a neoplastic context, making it a useful clinical target.
Publication Title
A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.
Sample Metadata Fields
Specimen part
View Samples