Microarray analysis of transcriptional changes in MeJA-treated tobacco leaves
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE182794 | GEO | 2022/05/31
REPOSITORIES: GEO
Similar Datasets
Project description:Microarray analysis of transcriptional changes in MeJA-treated tobacco leaves
| PRJNA757833 | ENA
Project description:Here we performed a transcriptomic study on complete symptom development process of CMV-infected Nicotiana tabacum using Solexa/Illumina's high-throughput digital gene expression (DGE) system. 12 DGE libraries (from six virus-infected samples and six corresponding mock-inoculated samples) were constructed, and the gene expression variations between the virus-infected sample and the mock-inoculated sample in each symptom stage were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes (such as phtosynthesis, pigment metabolism and plant-pathogen interaction) were related to the symptom development. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. We sequenced a cDNA library constructed from mixture of total RNA from six virus-infected samples and six mock-inoculated samples to get gene information for tobacco leaves in different symptom stages, including vein clearing, mosaic, severe chlorosis, partial recovery, total recovery and re-mosaic, and 95,916 Unigenes were obtained
2012-11-09 | GSE30162 | GEO
Project description:Here we performed a transcriptomic study on complete symptom development process of CMV-infected Nicotiana tabacum using Solexa/Illumina's high-throughput digital gene expression (DGE) system. 12 DGE libraries (from six virus-infected samples and six corresponding mock-inoculated samples) were constructed, and the gene expression variations between the virus-infected sample and the mock-inoculated sample in each symptom stage were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes (such as phtosynthesis, pigment metabolism and plant-pathogen interaction) were related to the symptom development. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. We sequenced a cDNA library constructed from mixture of total RNA from six virus-infected samples and six mock-inoculated samples to get gene information for tobacco leaves in different symptom stages, including vein clearing, mosaic, severe chlorosis, partial recovery, total recovery and re-mosaic, and 95,916 Unigenes were obtained Tobacco leaves were inoculated by CMV-infected leaf homogenate and healthy leaf homogenate, respectivley. Six time points with different symptom stage were selected, and one virus-infect sample and one mock-inoculated sample were collected at each time. In order to average out variation of different plants, five leaves from five different plants were mixed to prepare every RNA sample. Twelve individual tag libraries of samples (six infected samples and six mock-inoculated samples) were constructed in parallel. For the gene expression analysis, the twelve samples were grouped into six groups, and each group contained a virus-infected sample and a mock-inoculated sample collected at the same time. In each group, the DGE data of virus-infected sample were compared to that of mock-inoculated sample to obtain the gene expression variations. Illumina sequencing of transcripts from virus-infected and mock-inoculated samples to get gene information for tobacco leaves in different symptom stages. In order to get more gene information, the systemically infected leaves and mock-inoculated leaves were harvested at six time points and five leaves from five different plants were collected at each time point. The RNA-Seq analysis provided gene information for mock-inoculated and virus-infected tobacco leaves in different symptom stages.
2012-11-09 | E-GEOD-30162 | biostudies-arrayexpress
Project description:To understand signal transduction mechanism by MeJA in rice, we have analyzed transcription profile with 60K Rice Whole Genome Microarray after MeJA treatment. Gene transcripts were extracted from ten individual rice plants treated with 100 uM MeJA for 6 hrs. RNA samples from these plants were used to generate cyanine-3 (Cy3) and Cy5-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats independently.
2011-01-01 | GSE22757 | GEO
Project description:We used Affymetrix 1.0 ST arrays to compare the transcriptome of 4 weeks‐day‐old plants sprayed with 250uM of MeJA or mock (control). For the experiments we used wild-type (Col-0), phyB-9 and jaz10 single mutants and jaz10phyb double mutant. Samples were harvested after 3hours of induction with MeJA or mock. We performed a first analysis with the transcriptomes of wild‐type (Col-0) to identify those group of genes that are up‐ and down‐regulated by MeJA treatment (2 fold-changes). We founded 719 genes whose expression was statistically significantly different between the two treatments. To gain knowledge into the regulation of phyB over these set of 719 genes, we contrasted their expression levels against phyB transcriptome. By cluster analysis, we identified five major groups of genes, where in two of them the transcript levels increased in presence of MeJA (clusters 1 and 2) and three whose expression decrease after MeJA treatment (Cluster 3, 4 and 5).
2020-01-01 | GSE130255 | GEO
Project description:Comparative analysis of tobacco leaves transcriptomes unveils carotenoid pathway potentially determined the characteristics of aroma compounds in different environmental regions. Tobacco (Nicotiana tabacum) is a sensitive crop to environmental changes, and a tobacco with unique volatile aroma fractions always formed in specific ecological conditions. In order to investigate the differential expressed genes caused by environmental changes and reveal the formation mechanism of characteristics of tobacco in three different aroma tobacco regions of Guizhou Province, Agilent tobacco microarray was adapted for transcriptome comparison of tobacco leaves in medium aroma tobacco region Kaiyang and light aroma tobacco regions Weining and Tianzhu. Results showed that there was big difference among the gene expression profiles of tobacco leaves in different environmental conditions. A total of 517 differential expressed genes (DEGs) between Weining and Tianzhu were identified, while 733 and 1,005 genes differentially expressed between Longgang and another two tobacco regions Weining and Tianzhu, respectively. Compared with Longgang, up-regulated genes in Weining and Tianzhu were likely involved in secondary metabolism pathways, especially carotenoid pathway, including PHYTOENE SYNTHASE, PHYTOENE DEHYDROGENASE, LYCOPENE ε-CYCLASE, CAROTENOID β-HYDROXYLASE and CAROTENOID CLEAVAGE DIOXYGENASE 1 genes, while most down-regulated genes played important roles in response to temperature and light radiation, such as heat shock proteins. Gene Ontology and MapMan analyses demonstrated that the DEGs among different environmental regions were significantly enriched in light reaction of photosystem II, response of stimulus and secondary metabolism, suggesting they played crucial roles in environmental adaptation and accumulation of aroma compounds in tobacco plants. Through comprehensive transcriptome comparison, we not only identified several stress response genes in tobacco leaves from different environmental regions but also highlighted the importance of carotenoid pathway genes for characteristics of aroma compounds in specific growing regions. Our study primarily laid the foundation for further understanding the molecular mechanism of environmental adaptation of tobacco plants and molecular regulation of aroma substances in tobacco leaves.
2012-02-23 | GSE36008 | GEO
Project description:microbial communities on cigar tobacco leaf
| PRJNA741203 | ENA
Project description:To shed light on the biosynthesis mechanisms of these diterpenes, we performed the first high-throughput RNA-seq for A. paniculata leaves with time-serialized MeJA treatments. The transcriptomic approach not only defined a comprehensive transcriptome (comprised of 20,629 highly expressed genes), but also profiled time-serialized gene expression patterns with 4,463 up-regulated genes and 6,517 down-regulated genes responding to MeJA induction. These up-regulated genes significantly enriched in biological processes like stress responses, metabolic pathways, and secondary metabolites biosynthesis, especially terpene/terpenoid metabolic process. Consistent with the gradual accumulation of andrographolide, the expression of most genes involved in MEP pathway showed progressive increase. In the hypothetical terpenoid metabolism pathway, ApCPS2, which was putatively involved in andrographolide synthesis, dramatically increased its expression. Among other co-regulated genes, 154 genes encode cytochrome P450s (CYP450s); 42 genes were predicted as UDP glycosyltransferases (UGTs); and 363 genes belong to transcription factors.
2018-12-31 | GSE83775 | GEO
Project description:Transcriptional profiling of MeJA-treated pearl millet seedlings over time [0, 12, 24 and 48 hours post treatment (hpt)]. Keywords: Time course, Stress response
2009-01-01 | GSE13478 | GEO
Project description:Purpose: Understanding of MeJA, CK effect on regulation of gene expression patterns in Arabidopsis roots Total mRNA was extracted from 7-day-old Arabidopsis roots grown in MeJA (10uM), CK (50nM) and MeJA/CK-treated conditions. To generate cDNA libraries with TruSeq RNA library kit, 1 μg of total RNA was used. This step consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina HiSeq2000. 4,403 genes satisfying |fold change|â¥2 in at least one data set were collected.
2016-07-30 | E-GEOD-80188 | biostudies-arrayexpress