Expression analysis of abiotic stress-treated rice
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE31874 | GEO | 2012/03/01
SECONDARY ACCESSION(S): PRJNA145065
REPOSITORIES: GEO
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Project description:For identification of genes up-regulated in abiotic stress (drought, high salinity, low temperature and ABA) treated rice, total RNA (100 ?g) was prepared from root tissues of 14-d-old rice seedlings (Oryza sativa cv Nakdong) grown under normal growth conditions. For the high salinity and ABA treatments, the 14-d-old seedlings were transferred to a nutrient solution containing 400 mM NaCl or 100 ?M ABA for 2 h in the greenhouse under continuous light of approximately 1000 ?mol m-2 s -1. For drought treatment, 14-d-old seedlings were air-dried for 2 h also under continuous light of approximately 1000 ?mol m-2 s -1. For low temperature treatments, 14-d-old seedlings were exposed at 4°C in a cold chamber for 6 h under continuous light of 150 ?mol m-2 s -1. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in abiotic stress treated rice. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
2012-03-01 | E-GEOD-31874 | biostudies-arrayexpress
Project description:There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates. For 12 organs, three lines of plants were grown in soil under the long-day conditions of 16 hours light at 22℃. Samples were collected from each of juvenile rosette leaves, adult rosette leaves, cauline leaves, stems, young flower buds (sepals were closed and petals are not visible), mature flower buds (petals are visible), flowers, young siliques filled with white seeds, mature siliques filled with green seeds, old yellowing siliques (2-month-old) and senescence rosettes. Root tissues were collected from 2-week-old plants growing on 1% agar plates containing Murashige and Skoog (MS). Callus were collected from cultured CIM (callus induction medium) containing B5 medium supplemented with 20 g liter–1 glucose, 0.5 mg liter–1 2,4-D, and 0.1 mg liter–1 kinetin. Dry seed was defined to be after-ripened seeds for 4 weeks. Imbibed seeds are collected from seeds imbibed on the moistened paper for 24 and 48 hours under the continuous light at 22℃. In light irradiations, wild type (WT) seeds were plated on MS plates. For the time course experiment of white light, the plates were placed at 4°C in darkness for at least 2 days prior to receiving 6 h red light irradiation to synchronize germination. Then, plates were placed in the dark for 3 days and then exposed to white fluorescent light (100 μmol m–2 s–1) for 1, 6 and 24 h. For monochromatic light experiment, WT seedlings were grown in continuous red light, blue light, far-red light, or darkness for 6 days after red light irradiation. The light intensity used was 0.17 μmol m–2 s–1 for red light, 1.16 μmol m–2 s–1 for blue light and 0.53 μmol m–2 s–1 for far-red light. All abiotic stress samplings were collected from plants grown for 2 weeks on MS plates under 2 and 6 hours of abiotic stress conditions at the continuous light at 22℃. For drought stress treatment, plants were transferred and dehydrated onto the dried filter paper in the covered plastic dishes. For heat and cold stress treatments, the covered plastic dishes with plants were transferred directly from 22 to 37 and 2℃ respectively. For salinity stress treatment, plants were transferred onto the filter paper moistened with MS plates including 200mM NaCl.
2012-09-30 | E-GEOD-34188 | biostudies-arrayexpress
Project description:We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes under various stress conditions and plant hormone treatments. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. Three-week-old seedlings were used for all abiotic and biotic treatments. For heat or cold treatment, the seedlings were subjected to 35 ± 1 °C or 4 ± 1 °C conditions, respectively. The samples for RNA extraction were collected at 0, 1, 2, 4, and 8 h after treatment. For dehydration treatment, the leaves of plants were sampled at 0, 2, 4, and 6 d after watering stopped. For disease treatment, Pseudoperonospora cubensis (P.cubensis) was used to infect the seedlings, and leaves were collected at 0, 1, 2, and 3 d after infection. For hormone treatments, the seedling leaves were sprayed with 100 mM methyl jasmonate (meJA) or 100 mM abscisic acid (ABA) and then sampled at 0, 1, 2, 4, and 8 h intervals. The experiment was designed to examine the transcription patterns of 58 MAPK cascade genes in cucumber in response to three different abiotic stresses (cold, heat, and drought), one biotic stress (Pseudoperonospora cubensis) and two (MeJA and ABA) plant hormone treatments.
2015-05-01 | E-GEOD-68436 | biostudies-arrayexpress
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response
2008-11-19 | GSE9646 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response Two-week-old Arabidopsis plants grown on the agar plates were subjected to the stress- or ABA- treatments. The total RNA was prepared from the treated- and untreated- plants, and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.
2008-11-19 | E-GEOD-9646 | biostudies-arrayexpress
Project description:We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes under various stress conditions and plant hormone treatments. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. Three-week-old seedlings were used for all abiotic and biotic treatments. For heat or cold treatment, the seedlings were subjected to 35 ± 1 °C or 4 ± 1 °C conditions, respectively. The samples for RNA extraction were collected at 0, 1, 2, 4, and 8 h after treatment. For dehydration treatment, the leaves of plants were sampled at 0, 2, 4, and 6 d after watering stopped. For disease treatment, Pseudoperonospora cubensis (P.cubensis) was used to infect the seedlings, and leaves were collected at 0, 1, 2, and 3 d after infection. For hormone treatments, the seedling leaves were sprayed with 100 mM methyl jasmonate (meJA) or 100 mM abscisic acid (ABA) and then sampled at 0, 1, 2, 4, and 8 h intervals.
2015-05-01 | GSE68436 | GEO
Project description:Jasmonates (JA) and abscisic acid (ABA) are phytohormones known to play important roles in plant response and adaptation to various abiotic stresses including salinity, drought, wounding, and cold. JAZ (JASMONATE ZIM-domain) proteins have been reported to play negative roles in JA signaling. However, direct evidence is still lacking that JAZ proteins regulate drought resistance. In this study, OsJAZ1 was investigated for its role in drought resistance in rice. Expression of OsJAZ1 was strongly responsive to JA treatment, and it was slightly responsive to ABA, salicylic acid, and abiotic stresses including drought, salinity, and cold. The OsJAZ1-overexpression rice plants were more sensitive to drought stress treatment than the wild-type rice Zhonghua 11 (ZH11) at both the seedling and reproductive stages, while the jaz1 T-DNA insertion mutant plants showed increased drought tolerance compared to the wild-type plants. The OsJAZ1-overexpression plants were hyposensitive to MeJA and ABA, whereas the jaz1 mutant plants were hypersensitive to MeJA and ABA. In addition, there were significant differences in shoot and root length between the OsJAZ1 transgenic and wild-type plants under the MeJA and ABA treatments. A subcellular localization assay indicated that OsJAZ1 was localized in both the nucleus and cytoplasm. Transcriptome profiling analysis by RNA-seq revealed that the expression levels of many genes in the ABA and JA signaling pathways exhibited significant differences between the OsJAZ1-overexpression plants and wild-type ZH11 under drought stress treatment. Quantitative real-time PCR confirmed the expression profiles of some of the differentially expressed genes, including OsNCED4, OsLEA3, RAB21, OsbHLH006, OsbHLH148, OsDREB1A, OsDREB1B, SNAC1, and OsCCD1. These results together suggest that OsJAZ1 plays a role in regulating the drought resistance of rice partially via the ABA and JA pathways.
2018-02-28 | GSE107425 | GEO
Project description:Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling Keywords: Light and abscisic acid treatment Expression data for wild-type, atmyc2, cop1-6, and atmyc2 cop1-6 seedlings under constant dark, blue-light and blue-light along with abscisic acid Ten-day-old Arabidopsis (wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant) seedlings grown under constant dark, constant blue-light (35 µmol/sec/m2), and constant blue-light along with ABA (0.5 µm) were used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.
2009-12-31 | E-GEOD-8955 | biostudies-arrayexpress
Project description:Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen.
2012-12-09 | GSE22519 | GEO
Project description:Abiotic stress is a major environmental factor that limits cotton growth and yield, moreover, this problem has become more and more serious recently and multiple stresses often occur simultaneously due to the global climate change and environmental pollution. We used microarrays to analyze the crosstalk of responsive genes to multiple abiotic stresses including ABA, cold, drought, salinity and alkalinity in cotton. Cotton seedlings with different abiotic stress treatment were selected at 14-day after germination for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify genes involved in diverse stresses including abscisic acid (A), cold (C), drought (M), salinity (N) and alkalinity (P) by comparative microarray analysis (3 biological replicates for each abiotic stress treatment).
2013-09-12 | E-GEOD-50770 | biostudies-arrayexpress