Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes
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PROVIDER: PRJNA121149 | ENA |
REPOSITORIES: ENA
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Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
2010-03-01 | GSE18822 | GEO
Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies. We hybridized cRNA purified from nodule, leaf, and root of common bean and soybean in, triplicate, to the soybean GeneChip (18 GeneChip hybridizations = 2 species x 3 organs x 3 replicates).
2010-03-07 | E-GEOD-18822 | biostudies-arrayexpress
Project description: Not available
| S-EPMC3017814 | biostudies-literature
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path
2012-07-01 | GSE37638 | GEO
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path This work presents the transcriptional profile of bean nodules, induced by strain Rhizobium tropici CIAT 899, under oxidative stress, generated experimentally by adding the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed.
2012-06-30 | E-GEOD-37638 | biostudies-arrayexpress
Project description:To dissect the gene regulatory networks operating during Scarlet Runner Bean seed development, we identified the binding sites genome-wide for transcription factor in Scarlet Runner Bean seeds during seed development using ChIP-seq
2020-07-13 | GSE153644 | GEO
Project description:Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. Bean leaf extract was obtained from healthy bean leaves. In this work we investigated the effect of bean leaf extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without extract from healthy bean leaves.
2009-03-03 | GSE14998 | GEO
Project description:The immunomodulatory effect of mung bean is mainly attributed to antioxidant properties of flavonoids; however, the precise machinery for biological effect on animal cells remains uncertain. The objective of this study was to understand the physiological change produced by mung bean consumption.
2017-04-06 | PXD005330 | Pride
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation. In this work we analyzed the effect of VHb-expressing R. etli CE3 in the symbiosis of common bean plants under oxidative stress experimentally generated by the addition of PQ for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST).
2016-06-15 | E-GEOD-83324 | biostudies-arrayexpress
Project description:250 adult T. urticae females from the London strain (grown on acyanogenic P. vulgaris cv. Prelude bean plants) were transferred to cyanogenic P. lunatus cv. 8078 bean plants. Thirty-five generations after the host transfer, total RNA was extracted from mites growing on both bean species (London and London-CYANO strain) and used in in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent) experiment to assess significantly differentially expressed genes (FC ≥ 2 and FDR-corrected p-value < 0.05) between mites grown on P. vulgaris (cv. Prelude) bean plants (London strain) and mites grown for 35 generations on P. lunatus (cv. 8078) bean plants (London-CYANO strain).
2014-04-30 | GSE50162 | GEO