Oryza alta cultivar:wild allotetraploid rice
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PROVIDER: PRJNA623162 | ENA |
REPOSITORIES: ENA
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Project description:Genome sequencing of wild rice Oryza alta accessions
| PRJDB4639 | ENA
Project description:Staphylococcus aureus lipoteichoic acid (aLTA) and Lactobacillus plantarum LTA (pLTA) engage the same Toll-like receptor 2 (TLR2) signaling pathway, but exert different effects on the innate immune/inflammatory responses. aLTA is the leading cause of gram-positive bacterial sepsis induced by S. aureus, whereas pLTA is considered as a promising therapeutic agent for pathogen-induced septic shock. The mechanisms underlying the different functions of aLTA and pLTA remain unclear. We used human oligo microarrays to investigate the transcriptomes of human THP-1 monocytes upon exposure to aLTA and pLTA. Differential gene expression profiles were observed between the aLTA- and pLTA-treated cells. The expression levels of 1301 genes in aLTA-treated cells were changed more than 2 fold. These genes are critically involved in immune/inflammatory responses, cell adhesion, cell signal transduction, transcription factors, anion transport, proteolysis and oxidative processes. Especially, a variety of genes that encode cytokines/chemokines and other related molecules such as those belonging to the IRAK, TRAF, NF-κB, and STAT families were remarkably up-regulated by aLTA stimulation. In contrast, the expression levels of only 93 genes were altered by more than 1.5 fold in pLTA-treated cells, and these genes are almost not correlative with immune/inflammatory responses and other related processes compared with those of aLTA-treated cells. The different functions of aLTA and pLTA were further compared with the differential expressions of a selected group of genes, i.e., IRAKs, TRAFs and some cytokines/chemokines through RT-PCR and ELISA assays. The gene expression of IRAK2 could be markedly induced by aLTA, but significantly inhibited by pLTA treatment. These results suggest that the different functions of aLTA and pLTA on innate immunity and inflammation might be due to their different effects on the expression of some genes related with the innate immune/inflammatory responses, such as IRAK2 etc.
2010-04-02 | GSE15512 | GEO
Project description:The associated files are mass spec data from individual fractions of mixed-bed ion exchange or size exclusion fractionations of native extract made from rice leaves (Oryza sativa, Kitaake cultivar).
2019-10-28 | PXD013213 | Pride
Project description:Oryza rufipogon cultivar:Dongxiang wild rice Raw sequence reads
| PRJNA641241 | ENA
Project description:Oryza rufipogon cultivar:Dongxiang Wild Rice Raw sequence reads
| PRJNA312733 | ENA
Project description:Staphylococcus aureus lipoteichoic acid (aLTA) and Lactobacillus plantarum LTA (pLTA) engage the same Toll-like receptor 2 (TLR2) signaling pathway, but exert different effects on the innate immune/inflammatory responses. aLTA is the leading cause of gram-positive bacterial sepsis induced by S. aureus, whereas pLTA is considered as a promising therapeutic agent for pathogen-induced septic shock. The mechanisms underlying the different functions of aLTA and pLTA remain unclear. We used human oligo microarrays to investigate the transcriptomes of human THP-1 monocytes upon exposure to aLTA and pLTA. Differential gene expression profiles were observed between the aLTA- and pLTA-treated cells. The expression levels of 1301 genes in aLTA-treated cells were changed more than 2 fold. These genes are critically involved in immune/inflammatory responses, cell adhesion, cell signal transduction, transcription factors, anion transport, proteolysis and oxidative processes. Especially, a variety of genes that encode cytokines/chemokines and other related molecules such as those belonging to the IRAK, TRAF, NF-κB, and STAT families were remarkably up-regulated by aLTA stimulation. In contrast, the expression levels of only 93 genes were altered by more than 1.5 fold in pLTA-treated cells, and these genes are almost not correlative with immune/inflammatory responses and other related processes compared with those of aLTA-treated cells. The different functions of aLTA and pLTA were further compared with the differential expressions of a selected group of genes, i.e., IRAKs, TRAFs and some cytokines/chemokines through RT-PCR and ELISA assays. The gene expression of IRAK2 could be markedly induced by aLTA, but significantly inhibited by pLTA treatment. These results suggest that the different functions of aLTA and pLTA on innate immunity and inflammation might be due to their different effects on the expression of some genes related with the innate immune/inflammatory responses, such as IRAK2 etc. We analyzed gene expression change by aLTA and pLTA in THP1 cell to find the active pathway and related biology function.
2010-04-02 | E-GEOD-15512 | biostudies-arrayexpress
Project description:One of the serious constraints to realize high level of rice crop productivity in Indian agriculture has been due to soil moisture stress (SMS) situation that growing plants often face. In order to increase or maintain the crop productivity in SMS situation our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SMS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogan and three Indian cultivar namely Oryza Nagina-22, Oryza IR20 and Oryza Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SMS condition. Global analysis of transcript profiling under SMS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the transcript profiling from five genotypes of rice under control, soil moisture stress and after recovery conditions during vegetative and grainfilling phase.Here in case of Nagina-22 we have taken grainfilling stage.
2016-04-01 | GSE49364 | GEO
Project description:Various rice tissues were collected and immediately frozen from Dongin cultivar (Oryza sativa L. japonica).
2022-12-31 | E-MTAB-11005 | biostudies-arrayexpress
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2013-08-20 | GSE49963 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2012-05-01 | GSE37650 | GEO