Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305103 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Differentially expressed genes between non-treated and salt-treated WT plants
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Project description:Expression data from WT and transgenic plants overexpressing cold-induced transcription factors
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Project description:Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
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Project description:We examined global expression profiles of 7-days old 35S-TrAP transgenic plants compared to Col-0 wild-type using an Affymetrix ATH1 GeneChip and identified 586 genes that are differentially expressed in the 35S-TrAP transgenic plants (q<0.005). Of these, 295 transcripts were elevated whereas 291 were reduced (Figure 2E). We performed real-time PCR and RNA blot assays to validate the microarray results for the differentially expressed genes (DEGs).
2015-09-29 | GSE73495 | GEO
Project description:wip overexpressing plants-Transcriptome analysis of WIP overexpressing plants
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Project description:analysis of npc48 overexpressing plants-Analysis of npc48 overexpressing plants.
| PRJNA107663 | ENA
Project description:Solanum lycopersicoides (LA2408), collected at higher altitudes (up to 3600 meters) than any of other solanum species, is a wild nightshade distant-allied to cultivated tomato. Many traits of Solanum lycopersicoides including cold tolerance, resistance to virus diseases and insect pests were previously confirmed. Thus, it is an ideal candidate plant for isolating cold-tolerance-related genes. In this study, we successfully cloned the full-length cDNA of the CBF1 gene from Solanum lycopersicoides which was designated as SsCBF1. In order to investigate the possible functions of SsCBF1 in plant growth and stress responses, we generated transgenic Arabidopsis overexpressing SsCBF1. We employed the RNA-seq approach to identify the differentially expressed genes between the two genotypes. Processing of RNA samples on the Illumina HiSeq 2000 system produced more than 20 million reads, each 100bp in length, encompassing 2.0 Gb of sequence data for each sample which was then mapped to the reference genome. The statistical analysis identified a total of 338 differentially expressed genes between Col-0 (WT) and transgenic Arabidopsis overexpressing SsCBF1 with the criteria of Q-value < 0.001 and fold change >2, among which 120 (35.5%) were up-regulated and 218 (64.5%) were down-regulated. RNA-sequencing was carried out using one transgenic line (35S:SsCBF1-11) and the Col-0 (WT) plants. Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial parts of 4-week-old seedlings grown in parallel under unstressed conditions. Materials from 20 plants of each genotype were pooled for RNA isolation.
2013-09-01 | E-GEOD-40482 | biostudies-arrayexpress
Project description:Gene expression in wild-type and transgenic plants overexpressing rice OsTOP6A1 gene
| PRJNA99187 | ENA
Project description:In plants, fatty acids are de novo synthesized predominantly in plastids fromacetyl-CoA. Although fatty acid biosynthesis has been biochemically well-studied, little isknown about the regulatory mechanisms of the pathway. Here, we show that overexpressionof the Arabidopsis (Arabidopsis thaliana) LEAFY COTYLEDON1 (LEC1) gene causesglobally increased expression of fatty acid biosynthetic genes, which are involved in keyreactions of condensation, chain elongation and desaturation of fatty acid biosynthesis. Inthe plastidial fatty acid synthetic pathway, over 58% of known enzyme-coding genes areupregulated in LEC1-overexpressing transgenic plants, including those encoding threesubunits of acetyl-CoA carboxylase, a key enzyme controlling the fatty acid biosynthesisflux. Moreover, genes involved in glycolysis and lipid accumulation are also upregulated.Consistent with these results, levels of major fatty acid species and lipids were substantiallyincreased in the transgenic plants. Genetic analysis indicates that the LEC1 function ispartially dependent on ABSCISIC ACID INSENSITIVE3, FUSCA3 and WRINKLED1 in theregulation of fatty acid biosynthesis. Moreover, a similar phenotype was observed intransgenic Arabidopsis plants overexpressing two LEC1-like genes of Brassica napus.These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate theexpression of fatty acid biosynthetic genes, thereby representing a promising target forgenetic improvement of oil-production plants. Experiment Overall Design: The pER8-LEC1 transgenic seedlings were germinated and grown in the presence of 10 µM estradiol for 4 days. The control sample was germinated and grown under the identical conditions without estradiol but containing 0.1% DMSO. Total RNA was prepared from fresh or frozen plant materials using the RNAeasy Plant Mini Kit (Qiagen China, Beijing). The first strand cDNA was synthesized, and then hybridized with the ATH1 oligonucleotide chips as described by the manufactureâs instructions (Affymetrix). The microarray hybridization data were collected and analyzed using related R (http://www.r-project.org/) packages provided by Bioconductor (http://www.biocoductor.org/). In brief, genes differentially expressed between wild type and mutant plants were selected by first removing âabsentâ genes which were never detected to be expressed in the experiments, then a two-side t-test was applied to remaining genes in order to test the expression difference between wide type and mutant plants. To avoid multiple testing problems, raw p-values were then adjusted into False Discovery Rate (FDR) using Benjamini and Hochberg approach. Finally, differentially expressed genes were defined as those FDR less than 0.2. Functional analysis of differentially expressed genes was carried out using the biological process category of Arabidopsis Gene Ontology. The hierarchical map of GO annotation was constructed according to the ontology tree provided by the Gene Ontology website (http://www.geneontology.com) as described previously (Zheng and Wang, 2008). Ontology categories that are significantly enriched among differentially expressed genes (hypergeometric test and FDR less than 0.1) were displayed as boxes in the map.
2008-10-25 | E-GEOD-12137 | biostudies-arrayexpress
Project description:Inorganic phosphate (Pi) is an essential nutrient, which is often served as a limiting factor in plant growth. It has been reported that SPL family members, such as SPL3, regulate Pi deficiency responses by controlling the expression of Pi deficiency responsive genes. To elucidate whether SPL9 respond to low phosphorus stress, we investigated the phenotypes and conduct RNA sequencing analysis in transgenic Arabidopsis thaliana with overexpressing SPL9 (R9) under conditions of both normal and low Pi availability. Compared with wild-type plants, R9 showed decreased anthocyanin accumulation and increased Pi contents in shoots under Pi deficiency. Through RNA-seq analysis compared with wild-type plants, we detected 217 genes significantly differentially expressed in conditions of Pi sufficiency, and 121 genes differentially expressed in conditions of Pi deficiency in R9 plants. Under Pi deficiency, these genes included multiple protein kinases, jasmonic acid response genes and genes related to salt stress responses. Genes associated with hydrolase and transferase activity were also differentially regulated by Pi deficiency, such as cytochrome P450 monooxygenases. Of particular note, the transcription factor AP2-EREBP and members of the bHLH family were among the most significantly differentially regulated genes identified under both Pi sufficient and Pi deficient conditions.
2021-09-03 | GSE183312 | GEO