Rice gene expression using Agilent custom 8X60K Microarray
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE48395 | GEO | 2013/10/18
SECONDARY ACCESSION(S): PRJNA209939
REPOSITORIES: GEO
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Project description:We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the expression divergence and regulation between two contrasting rice genotypes under high salinity stress. The expression analysis was carried out using 14-day old whole seedlings from both japonica and indica rice lines. Two samples from NaCl treatment (0h and 8h) for each line were collected for the analysis. Two biological replicates were carried out for both control and NaCl treatments, resulting in a dataset of 8 microarrays.
2013-10-18 | E-GEOD-48395 | biostudies-arrayexpress
Project description:We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the differentially expressed genes after over-expression of the rice gene with locus name LOC_Os02g43330.
2023-07-15 | GSE154469 | GEO
Project description:As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments
2012-04-08 | GSE36689 | GEO
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.
2015-11-02 | GSE58603 | GEO
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
2015-11-02 | E-GEOD-58603 | biostudies-arrayexpress
Project description:As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments The expression analysis was carried out using 14-day old whole seedlings from both grain and sweet sorghum lines. Three samples from sucrose treatment (0h, 2h and 6h) for each line were collected for the analysis . Two biological replicates were carried out for both control and sucrose treatments, resulting in a dataset of 12 microarrays.
2012-04-07 | E-GEOD-36689 | biostudies-arrayexpress
Project description:Background: Transcription factors (TFs), such as ERFs (Ethylene Responsive Factors), are important for regulating plant growth, development, and plant responses to abiotic stress. Notably, over half of the rice ERF-X group members are stress-responsive genes, including OsERF106. However, their regulatory roles in abiotic stress responses remain poorly understood. Results: The OsERF106, a salinity-induced gene of unknown function, was differently annotated in the RAP-DB and MSU RGAP. In this study, we isolated a novel (i.e., previously unannotated) OsERF106 gene and investigated its role in regulating growth and the response to salinity stress in rice. This OsERF106 is expressed in germinating seeds, primary roots, and developing flowers. Overexpression of the novel OsERF106 can cause a retardation of growth, a relatively high level of both MDA and ROS contents, a depression of CAT activity, and an overaccumulation of both Na+ and K+ ions in the transgenic rice shoots. Meanwhile, the expression of OsHKT1.3 is down-regulated in the shoots of transgenic seedlings grown under both normal and NaCl-treated conditions, while the expression of OsAKT1 is up-regulated in the same tissues grown under NaCl-treated conditions. Further analysis by microarray and qPCR indicated that the expression of several abiotic stress-responsive genes, such as OsABI5 and OsSRO1c, is also changed in the shoots of transgenic rice grown under either normal or NaCl-treated conditions. Conclusion: The novel OsERF106 negatively regulates shoot growth and salinity tolerance in rice through the disruption of ion homeostasis and modulation of stress-responsive gene expression.
2021-09-29 | GSE160238 | GEO
Project description:In order to understand molecular mechanisms of salt stress tolerance in rice several researches have been reported, however there are still unclear processes involved in salt tolerance. For reaching to a better perspective of the molecular mechanisms, we designed a comprehensive transcriptome study consisting contrasting genotypes, different tissues and different sampling time points. Two contrasting genotypes were selected and grown in Yoshida hydroponic medium for 14 days under controlled conditions. For salinity stress half of the seedlings were under 150 mM NaCl and after 6 and 54 h the treated and untreated samples were harvested in three replications from roots and shoots separately
2023-01-01 | GSE133480 | GEO
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor CBF2. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: genetic_modification_design
2006-08-15 | GSE5536 | GEO
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor ZAT12. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: genetic_modification_design
2007-01-08 | GSE5742 | GEO