Global gene expression in Atss3 mutant and WT over short day diurnal cycle
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE11708 | GEO | 2008/06/12
SECONDARY ACCESSION(S): PRJNA106003
REPOSITORIES: GEO
Similar Datasets
Project description:The Atss3 mutant and WT plants were arranged according to a Randomized Complete Block Design. The plants were planted in rows with seven rows in each flat; two plants of the same genotype/pot. Plants were grown under a SD photoperiod (8 h light/16 h dark) in a growth chamber as described. Eight randomly selected rows were harvested for each time point from different flats. Plant material was harvested at five time points in the diurnal cycle (1, 4, 8.5, 12, and 16 h; Time 0 is the beginning of the light period); harvesting was conducted under a green safety light. Each sample consisted of rosette leaves (leaves 5 to 8, staged following Bowmann (1994); photosynthetically active (Stessman et al., 2002)) from sixteen six-week-old plants. Leaf samples were frozen in liquid N2 immediately after harvest and stored at -80ï°C for RNA extraction. The experiment was done twice and independent randomizations for plant growth and harvest were used for the two replicates. Experiment Overall Design: The Atss3 mutant and WT plants were arranged according to a Randomized Complete Block Design. The plants were planted in rows with seven rows in each flat; two plants of the same genotype/pot. Plants were grown under a SD photoperiod (8 h light/16 h dark) in a growth chamber as described. Eight randomly selected rows were harvested for each time point from different flats. Plant material was harvested at five time points in the diurnal cycle (1, 4, 8.5, 12, and 16 h; Time 0 is the beginning of the light period); harvesting was conducted under a green safety light. Each sample consisted of rosette leaves (leaves 5 to 8, staged following Bowmann (1994); photosynthetically active (Stessman et al., 2002)) from sixteen six-week-old plants. Leaf samples were frozen in liquid N2 immediately after harvest and stored at -80ï°C for RNA extraction. The experiment was done twice and independent randomizations for plant growth and harvest were used for the two replicates.
2008-10-21 | E-GEOD-11708 | biostudies-arrayexpress
Project description:Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.]
2009-02-25 | GSE14930 | GEO
Project description:Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.] genotype: Mla6 - pathogen isolates: 5874 - time: 0(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 8(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 16(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 20(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 24(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 32(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 0(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 8(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 16(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 20(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 24(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 32(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 0(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 8(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 16(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 20(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 24(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 32(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 0(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 8(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 16(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 20(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 24(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 32(3-replications)
2009-02-25 | E-GEOD-14930 | biostudies-arrayexpress
Project description:Cotton seeds (Gossypium hirsutum cv. CCRI12) were grown in a growth chamber under 29/25°C temperature and a 16:8 h light:dark cycle, and water was added every two days. All plants were used in experiments at the 6-7 fully expanded true leaf stage, which occurred 5-6 weeks after sowing. Cotton bollworm (CBW; Helicoverpa armigera) larvae were reared on an artificial diet and maintained at 27 ± 2°C, 75 ± 10% relative humidity, and 14:10 h light:dark in the laboratory. For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 × 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed. For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 × 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed.
2016-01-01 | GSE62158 | GEO
Project description:Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown at 20˚C constant temperature, 8 hr/16 hr Light/Dark photoperiod at 50-60% ambient humidity, for 8 to 9 weeks. Short day conditions prevented the onset of flowering and the plants were thus maintained in growth stage 1 (leaf production) with 13 to 15 rosette leaves larger than 1mm (stage 1.13 to 1.14). Diamondback moth (DBM, Plutella xylostella) larvae were maintained on cabbage (Brassica oleracea) plants in a climate-controlled room at 25ºC, 12 hr photoperiod with 50%-60% relative humidity. Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). For insect treatment, seven Diamondback moth (DBM, Plutella xylostella) larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately. All rosette leaves were harvested at 1h, 4h, 12h, and 24h after onset of continuous herbivory and flash frozen in liquid nitrogen. Control plants were maintained under the same conditions and harvested in parallel. Keywords: time course, stress response, herbivory response
2008-03-04 | GSE10681 | GEO
Project description:Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive disease of wheat worldwide. Genetic resistance is the preferred method for controlling stripe rust, of which two major types are race-specific and race non-specific resistance. Race-specific resistance includes the qualitatively inherited all-stage resistance, controlled by single major resistance (R) genes. Conversely, adult-plant resistance is race non-specific, inherited quantitatively, and is durable. Previously, we characterized the gene expression signatures involved in Yr5-controlled all-stage resistance and Yr39-controlled adult-plant resistance using the Affymetrix Wheat GeneChip. For this study, we designed and constructed custom oligonucleotide microarrays containing probes for the 116 and 207 transcripts that we had found important for the Yr5 and Yr39 resistance responses, respectively. We used this custom microarray to profile the resistance responses of eight wheat genotypes with all-stage resistance (Yr1, Yr5, Yr7, Yr8, Yr9, Yr10, Yr15, and Yr17). The aim of this analysis was to identify common and unique gene expression signatures involved in race-specific resistance accross genotypes, which were used to infer information regarding the general pathways involved in all-stage resistance. Keywords: Stress response Eight wheat genotypes with defined single gene all-stage resistance to particular stripe rust (Pst) isolates were selected for this study, as well as the Pst susceptible genotype âAvocet Susceptibleâ (AVS). Near Isogenic Lines (NILs) for each of eight Yr resistance genes (Yr1, Yr5, Yr7, Yr8, Yr9, Yr10, Yr15 and Yr17) were developed at the Plant Breeding Institute, Sydney, Australia, by backcrossing the Yr gene donors with the recurrent susceptible spring wheat genotype (Triticum aestivum L.) AVS six times (AVS*6/Yr*) and selecting for the appropriate resistance at each generation. Both virulent and avirulent isolates of Pst were selected for each NIL, except for Yr15, for which no virulent isolate is currently known. Care was taken to select the fewest isolates needed to satisfy the spectrum of virulence/avirulence required, resulting in the use of six isolates identified as PST-17, PST-21, PST-43, PST-45, PST-78 and PST-AUS. Each isolate was selected and maintained on susceptible genotypes. For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate). Each flat consisted of three rows of six seedlings, with rows randomly assigned one of two harvest times (24 and 48 h post-inoculation). Seedlings from the 3rd row were used to monitor the expected disease responses to inoculation. Seedlings were grown to the second leaf stage (Feekes 1.2, emergence with second leaf unfolded, ~10 days after planting) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle. Inoculation was performed by misting the plants with sterile water and applying a 1:20 urediniospore:talc mixture to leaves with a sterile brush. Talc was used to aid in the spread and adhesion of spores over leaf surfaces. Control flats were treated the same way except for the absence of spores in the talc. All treatments for each biological replication were performed at 9 am Pacific Standard Time. To promote spore germination, all flats were transferred to a dew chamber (100% RH) operating at 10ºC in the dark for 24 h, before being placed in a growth chamber with a diurnal temperature cycle of 4ºC (2:00 am) to 20ºC (2:00 pm) and a 16 h light/8 h dark cycle. Rows of plants were harvested from all flats at the assigned times for RNA extraction.
2010-05-19 | E-GEOD-13346 | biostudies-arrayexpress
Project description:Potato cultivar Russet Norkotah was grown in a growth chamber at 16 hour light/8 hour dark at 22°C fertilized with Osmocote. Plants were from tissue culture, transplanted to soil and used approximately 4 weeks after transplanting. RNA was extracted from leaves using Trizol. Plants were sprayed with one of four treatments, either 1mM salicylic acid, 100 µM methyl jasmonate, 1 mg/ml arachidonic acid or 100 µM methyl jasmonate plus 1 mM salicylic acid together. Samples were harvested at 3, 24 and 72 hours after spraying. Each salicylic acid or arachidonic acid treatment has 3 biological replicates done in parallel, using leaves pooled from 2 plants. The control for SA or AA treated plants were water sprayed plants, from which leaves of 3 different plants were pooled at each timepoint, done side-by-side with the treated samples. Methyl jasmonate or MJ+SA treatments had 2 biological replicates each, using leaves pooled from 2 plants. A separate set of water sprayed plants (from the SA and AA control treatments) were used as controls, and pooled leaves from 3 plants were used at each time-point, and done in parallel with the treated samples. Keywords: Direct comparison
2007-09-01 | GSE8208 | GEO
Project description:Cuttings from Razegui cultivar were cultivated in sand for 2 months according to the method we have described previously (Azri et al. 2020). Then grapevine plantlets were further grown in pots containing sand/peat mixture (2/1, v/v), in a controlled greenhouse (16 h light/8 h dark at PAR 300 μmol m-2 s-1 photoperiod, 24 °C day/20 °C night temperature and 65-75% relative humidity). They were watered daily with tap water and supplemented once a week with 100 mL of Gibeaut’s nutrient solution (Gibeaut et al. 1997). Drought stress was applied according to our previously described procedure (Azri et al. 2020): plants with 10-15 leaves were either irrigated daily with water (control) or non-irrigated at all (water deficit). After 4 time points (day 0, 4, 8 and 16) of water deficit, the 4th fully-developed leaf was harvested and used for physiological analyses. Three independent biological experiments were performed consisting each in 2 treatments (control and water deficit) and 3 plants per time point and treatment. Proteomic analysis was performed on the 5th fully developed leaves at the time point 16 days of drought treatment. Irrigated and non-irrigated leaves were harvested immediately in liquid nitrogen and stored at - 80 °C until analysis. Three biological replicates were carried out for each treatment.
2021-08-06 | PXD027073 | Pride
Project description:Cotton seeds (Gossypium hirsutum cv. CCRI12) were grown in a growth chamber under 29/25°C temperature and a 16:8 h light:dark cycle, and water was added every two days. All plants were used in experiments at the 6-7 fully expanded true leaf stage, which occurred 5-6 weeks after sowing. Cotton bollworm (CBW; Helicoverpa armigera) larvae were reared on an artificial diet and maintained at 27 ± 2°C, 75 ± 10% relative humidity, and 14:10 h light:dark in the laboratory. For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 Ã? 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed. For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 Ã? 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed. In this study we present dynamic transcriptome analysis and volatile profiling of cotton plants fed upon by larvae of a leaf-chewing herbivore CBW. Plant transcriptomic changes induced by CBW were analyzed using Affymetrixâ??s Cotton GeneChips. Samples from a time course of six hour to 48 hours following onset of CBW feeding were analyzed to identify target genes and key pathways involved in the activation of herbivory-induced indirect defense and to explore genetic basis of such defense. In addition, we monitored the accumulation of VOCs, which represent changes in cotton plant phenotype, following CBW infestation.
2016-07-03 | E-GEOD-62158 | biostudies-arrayexpress
Project description:au08-04_dfo - analysis of deferoxamine treated leaves and roots - What are the effects of the siderophore deferoxamine on Arabidopsis leaves and roots? - Plants were allowed to grow for 5-6 weeks. The nutrient solution contains 0.25 mM Ca(NO3)2.4H2O, 1mM KH2PO4, 0.5 mM KNO3, 1mM MgSO4.7H2O, 50 µM H3BO3, 19 µM MnCl2.4H2O, 10 µM ZnCl2, 1 µM CuSO4.5H2O, 0.02 µM Na2MoO4.2H2O and 50 µM FeNa-EDTA. Plants were subjected to an 8 h light/16 h dark cycle, at 19°C, with 70% relative humidity. Leaves of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves were harvested 7 and 24 h.p.i. Keywords: time course,treated vs untreated comparison
2010-06-01 | GSE18976 | GEO