Transcription profiling by array of alfafa seedlings exposed to Arsenic (V)
Ontology highlight
ABSTRACT:
ORGANISM(S): Medicago sativa
SUBMITTER: Belén Montero
PROVIDER: E-MTAB-2158 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:After 24 h of acclimatisation Medicago sativa seedlings were treated with HgCl2 diluted on fresh MS to a final concentration of 3 uM during 3, 6 and 24 h.
2014-03-03 | E-MEXP-3876 | biostudies-arrayexpress
Project description:To identify putative regulatory elements enriched in the promoters of target genes of the PGE-dependent retrograde signaling pathway, we analyzed 500 bp regions of sequence upstream of genes whose expression was down-regulated by lincomycin. We treated dark-grown Arabidopsis seedlings with lincomycin, sampled them before or after a short illumination and examined the genomic response using Affymetrix ATH1 oligonucleotide microarrays. Differentially regulated genes were ranked based on descending degree of significance (p-value) and the top 50 genes affected by lincomycin in dark grown seedlings and top 50 genes affected by the antibiotic after illumination were selected for further analysis. Experiment Overall Design: 2*2 factorial design, two variables are (1) with/without lincomycin treatment (2) with/without red illumination. There are 2 replicates for each condition.
2008-06-14 | E-GEOD-5759 | biostudies-arrayexpress
Project description:Camptothecin (CPT) is a plant alkaloid that specifically binds topoisomerase I (Topo I) inhibiting its activity and inducing double stranded breaks in the DNA, activating the genotoxic cell responses, and ultimately, it might trigger programmed cell death (PCD). We used microarrays to detail the changes in gene expression during as a consequence of CPT treatment in maize immature embryos. In four independent experiments immature embryos were plated on MS medium supplemented with 50 uM CPT and incubated during three days. Untreated embryos incubated on MS medium were used as controls.
2010-11-01 | E-MEXP-2702 | biostudies-arrayexpress
Project description:This study investigates the mechanisms employed by Salmonella to colonise and establish itself on fresh produce at critical timepoints following infection. We established an alfalfa infection model and compared the findings to those obtained from glass surfaces. Our research revealed dynamic changes in the pathways associated with biofilm formation over time, with distinct plant-specific and glass-specific mechanisms for biofilm formation, alongside the identification of shared genes playing pivotal roles in both contexts.
2023-11-24 | E-MTAB-13495 | biostudies-arrayexpress
Project description:Determining the role of the Mediator subunit MED25/PFT1 in coordinating the expression of glucose responsive genes in Arabidopsis thaliana
2014-03-01 | E-MTAB-2297 | biostudies-arrayexpress
Project description:Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h. Experiment Overall Design: Arabidopsis thaliana ecotype Columbia glabra (gl1-1) was used in this study. Seeds were sterilized with diluted bleach (10 min incubation in 1.7% sodium hypochlorite, rinsing and washing thoroughly in sterile water), and incubated in 2.5 ml liquid growing medium [Murashige-Skoog (MS) half strength solution] in 6-well plates (fully aerobic, with shaking). Plates were incubated in the darkness at 4°C for 2 days and finally transferred to 23°C for 4 days before the sugar treatments (with 90 mM sucrose, lasting 6h). Two independent, replicated experiments were performed for sucrose treatments. Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction. Experiment Overall Design: AIR EXPERIMENT 1: Control without added sucrose Experiment Overall Design: AIR EXPERIMENT 2: Control without added sucrose Experiment Overall Design: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 1 Experiment Overall Design: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 2
2008-06-12 | E-GEOD-3704 | biostudies-arrayexpress
Project description:Using meDIP-chip to provide methylation profile in zdp mutant and identify hypermethylated regions comparing to wild type Arabidopsis plants. Examination of zdp mutant's methylome. 4 samples(1 mutant, 1 WT, each has two biological replicates)
2012-03-20 | E-GEOD-33719 | biostudies-arrayexpress
Project description:Arabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.
2011-05-18 | E-MEXP-2714 | biostudies-arrayexpress
Project description:Boron is an essential micronutrient for plants and is taken up in the form of boric acid (BA). Despite this, a high BA concentration is toxic for the plants, inhibiting root growth and is thus a significant problem in semi-arid areas in the world. In this work, we report the molecular basis for the inhibition of root growth caused by boron. We used microarrays to detail the global gene expression underlying boron toxicity in roots. 5-day-old arabidopsis plants were transferred to medium with high boron concentration (½ MS medium supplemented with 5mM BA) and control conditions (½ MS medium). We determined that 5 mM BA is the minimum concentration that produces the maximum effect, stunting root growth by ~50% after 5 days as compared with control conditions. We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array). We compared the transcripts obtained at 12 hrs of BA treatment.
2011-11-01 | E-GEOD-32659 | biostudies-arrayexpress
Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Two samples (TSA-treated v.s. untreated). Two replicates for each sample.
2008-06-12 | E-GEOD-3783 | biostudies-arrayexpress