E-ENAD-4
Ontology highlight
ABSTRACT:
PROVIDER: E-ENAD-4 | ExpressionAtlas | 2017-12-05
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-ENAD-4-analysis-methods.tsv | Tabular | |||
| E-ENAD-4-analytics.tsv | Tabular | |||
| E-ENAD-4-atlasExperimentSummary.Rdata | Rdata | |||
| E-ENAD-4-configuration.xml | Xml | |||
| E-ENAD-4-g7_g1-mvaPlot.png | Other |
Items per page: 5 1 - 5 of 77 |
Similar Datasets
Project description:Cellulase, a Type II secretion system secreted protein of Xanthomonas oryzae pv. oryzae (Xoo; the casual of bacterial leaf blight of rice) is a potent inducer of rice defense responses such as hypersensitive response like reactions (HR), callose depositions, cell death associated with nuclear fragmentations and impart functional resistance against further Xoo inoculation In order to understand the molecular events associated with cellulase induced HR in rice, whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips Keywords: Expression profiling of a hypersensitive reaction like response
2009-12-24 | GSE8216 | GEO
Project description:Four L. sativus accessions, exhibiting varying levels of resistance to E. pisi (resistant, partially resistant, partially susceptible, and susceptible), were analysed using dual RNA-seq. Leaflets from each plant were sampled at 0 (non-inoculated), 6, 12, 24, 48, and 72 hours after inoculation. Forty six samples were sequenced by lllumina Novaseq PE150 at STABvida sequencing provider (Lisbon, Portugal).
2025-02-28 | E-MTAB-14647 | biostudies-arrayexpress
Project description:Natural variation within plant species is an important resource for discovery of genes controlling biological traits. Gene-expression profiling of natural variation is increasingly used to identify genes affecting a trait. Here, we explored variation among Arabidopsis thaliana accessions with respect to defense against Pseudomonas syringae pv. tomato DC3000 (Pst), with a focus on R-gene mediated resistance triggered by the Pst type III effector protein AvrRpt2. We explored variation at two phenotypic levels: growth of the bacteria and hypersensitive response (HR) measured by electrolyte leakage. Considerable variation among accessions was found at both phenotypic levels. The genetic variation among accessions affected both growth of Pst with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector, with some variation being specific for the bacterial strains, and other variation affecting both strains in a similar manner. Variation in HR was not correlated with variation in bacterial growth. Additionally we examine variation in gene-expression profiles after mock- and Pst avrRpt2-inoculated plants, obtained using a dedicated microarray Gene-expression profiling at 6 h post inoculation identified clusters of genes from which expression levels are correlated with bacterial growth and electrolyte leakage. The expression levels of some of these clusters correlate with more than one phenotypic characteristic, such as growth of both Pst and Pst avrRpt2, whereas other clusters were correlated with just one biological parameter. Thus we demonstrate that variation in gene-expression profiles among Arabidopsis accessions is correlated with variation in phenotypic responses. Keywords: Comparisons of Arabidopsis thaliana accessions with respect to inoculation with Pseudomonas syringae pv tomato avrRpt2.
2007-08-09 | GSE8298 | GEO
Project description:Cellulase, a Type II secretion system secreted protein of Xanthomonas oryzae pv. oryzae (Xoo; the casual of bacterial leaf blight of rice) is a potent inducer of rice defense responses such as hypersensitive response like reactions (HR), callose depositions, cell death associated with nuclear fragmentations and impart functional resistance against further Xoo inoculation In order to understand the molecular events associated with cellulase induced HR in rice, whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips Keywords: Expression profiling of a hypersensitive reaction like response Leaves of 20 days old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo cellulase (5μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.0) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12 h after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo cellulase and the buffer
2009-12-24 | E-GEOD-8216 | biostudies-arrayexpress
Project description:Responses of Arabidopsis immune signaling mutants to Alternaria brassicicola infection
2015-12-01 | E-GEOD-50526 | ExpressionAtlas
Project description:Transcript profiling during susceptible (S) and HR-associated resistance (R) responses was determined in soybean (Glycine max). Pseudomonas syringae pv. glycinea carrying or lacking the avirulence gene avrB, was infiltrated into cultivar Williams 82. Leaf RNA was sampled at 2, 8, and 24 hours post inoculation (hpi). Significant changes in transcript abundance were observed for 3,897 genes during the experiment at p = 0.000005. Many of the genes showed a similar direction of increase or decrease abundance in both the S and R responses, but the R response generally showed a significantly greater degree of differential expression. More than 25% of these responsive genes had not been previously reported as being associated with pathogen interactions, as 704 had no functional annotation and 378 had no homolog in NCBI databases. The highest number of transcriptional changes was noted at 8 hpi including the down regulation of 94 chloroplast-associated genes specific to the R response. Photosynthetic measurements were consistent with an R-specific reduction in photosystem II operating efficiency (FPSII) that was apparent at 8 hpi for the R response with little effect in the S or control treatments. Imaging analyses suggest that the decreased FPSII was a result of physical damage to PSII reaction centers. Keywords = compatible Keywords = disease Keywords = genomic Keywords = hypersensitive response Keywords = incompatible Keywords = plant Keywords: susceptible vs resistant
2005-07-21 | GSE2961 | GEO
Project description:Background. Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumes in the semi-arid tropics. While most cowpea accessions are susceptible to the root parasitic weed Striga gesnerioides, several cultivars have been identified that show race-specific resistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S. gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots of cultivar B301 develop a strong resistance response characterized by a hypersensitive reaction and cell death at the site of parasite attachment. In contrast, no visible response occurs in B301 roots parasitized by SG4z. Results. Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, were investigated at 6 and 13 days post-inoculation (dpi), in the early and late stages of the resistance response using a Nimblegen custom design cowpea microarray. A total of 111 genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102 genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed during compatible (susceptible) interactions of B301 with SG4z . Genes and pathways involved in signal transduction, programmed cell death and apoptosis, and defense response to biotic and abiotic stress were differentially expressed in the early resistance response; at the later time point, enrichment was primarily for defense-related gene expression, and genes encoding components of lignifications and secondary wall formation. In compatible interactions (B301 M-bM-^@M-^S SG4z), multiple defense pathways were repressed, including those involved in lignin biosynthesis and secondary cell wall modifications, while cellular transport processes for nitrogen and sulfur were increased. Conclusion. Distinct changes in global gene expression profiles occur in host roots following successful and unsuccessful attempted parasitism by Striga. Induction of specific defense related genes and pathways defines components of a unique resistance mechanism. Some genes and pathways up-regulated in the host resistance response to SG3 are repressed in the susceptible interactions, suggesting that the parasite is targeting specific components of the hostM-bM-^@M-^Ys defense. These results add to our understanding of plant-parasite interactions and the evolution of resistance to parasitic weeds. A Nimblegen custom design cowpea microarray investigating gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, at 6 and 13 days post-inoculation (dpi), in the early and late stages of the resistance response.
2012-09-20 | E-GEOD-39348 | biostudies-arrayexpress
Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240964 | GEO
Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240965 | GEO
Project description:tri38-lar - hr - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Here, we want to analyse the transcriptome of Arabidopsis thaliana developing HR. To achieve this, we used Col0 leaf tissues developing an HR reaction after inoculation of the avirulent strain of PstDC3000 carrying the gene avrRpm1. Keywords: normal vs disease comparison
2008-12-01 | GSE13389 | GEO