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Transcription profiling of rice plants under the Md3 (pF3.5) condition in shoots

ABSTRACT: In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Md3-treated rice seedling shoots.
Md3 (Mild drought level 3): We designated Md3 as a term that means the level of drought severity corresponding to pF3.5, which is equal to a soil matric potential of -155.3 kPa. pF3.5: The value of pF shows the soil matric potential of -155.3 kPa.

ORGANISM(S): Oryza sativa

SUBMITTER: Junya Mizoi

PROVIDER: E-MTAB-4136 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of rice plants under the Md3 (pF3.5) condition in shoot basal region

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Md3-treated rice seedling shoot basal region. Md3 (Mild drought level 3): We designated Md3 as a term that means the level of drought severity corresponding to pF3.5, which is equal to a soil matric potential of -155.3 kPa. pF3.5: The value of pF shows the soil matric potential of -155.3 kPa.

2016-12-26 | E-MTAB-4140 | biostudies-arrayexpress

Transcription profiling of rice plants under the Md2 (pF2.5) condition in shoots

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Md2-treated rice seedling shoots. Md2 (Mild drought level 2): We designated Md2 as a term that means the level of drought severity corresponding to pF2.5, which is equal to a soil matric potential of -31.0 kPa. pF2.5: The value of pF shows the soil matric potential of -31.0 kPa. pF is an index that is equivalent to the effort required for plant root systems to extract water stored in soil.

2016-12-26 | E-MTAB-4135 | biostudies-arrayexpress

Transcription profiling of rice plants under the Md2 (pF2.5) condition in shoot basal region

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Md2-treated rice seedling shoot basal region. Md2 (Mild drought level 2): We designated Md2 as a term that means the level of drought severity corresponding to pF2.5, which is equal to a soil matric potential of -31.0 kPa. pF2.5: The value of pF shows the soil matric potential of -31.0 kPa. pF is an index that is equivalent to the effort required for plant root systems to extract water stored in soil.

2016-12-26 | E-MTAB-4139 | biostudies-arrayexpress

Transcription profiling of rice plants under the Sds (severe drought in soil) condition in shoot basal region

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Sds-treated rice seedling shoot basal region. Sds (Severe dehydration stress in soil containers): We designated Sds as a term that means a severe drought stress causing dehydration of plants in our experiments (The plants were dehydrated at the sampling point). The drought stress was achieved by withholding water from plants grown in soil containers.

2016-12-26 | E-MTAB-4141 | biostudies-arrayexpress

Transcription profiling of rice plants under the Sds (severe drought in soil) condition in shoots

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Sds-treated rice seedling shoots. Sds (Severe dehydration stress in soil containers): We designated Sds as a term that means a severe drought stress causing dehydration of plants in our experiments (The plants were dehydrated at the sampling point). The drought stress was achieved by withholding water from plants grown in soil containers.

2016-12-26 | E-MTAB-4138 | biostudies-arrayexpress

Transcription profiling of rice plants under the Sda (Air-drying) condition in shoots

Project description:In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Sda-treated rice seedling shoots. Sda (Severe dehydration stress by air drying): We designated the Sda as a term that means a dehydration stress in our experiments. The dehydration stress treatment was carried out by pulling plants from the soil and leaving them on a bench.

2016-12-26 | E-MTAB-4137 | biostudies-arrayexpress

differential gene expression dynamics of Pseudomonas putida KT2440 under matric stress

Project description:Our first aim was understand whole genome expression dynamics of Pseudomonas putida KT2440 surface colonies under water stress. Therefore, we wanted to identify significantly differentially expressed genes of at -0.4 MPa matric potential relative to the -0.5 kPa (near saturation condition) at different stress durations. Aliquots of overnight grown P. putida KT2440 cells were inoculated (approx. 100 µl and 1x107 cells) on the surface of ceramic plates. Prior to matric stress, the cells were incubated for 120, 116, 96, and 48 hr at-0.5 kPa to allow formation of a mature cell loan. -0.4 MPa matric potential was applied for the last 0 (control), 4, 24, and 72 hr of incubation periods, respectively, so that the total incubation time (at (-0.5 kPa) and (-0.4 MPa)) was kept constant as 5 days. Our second aim was to find out how the gene expression profile would change when we use PEG-8000 to simulate matric stress. To that effect, similar incubations were performed where the direct matric potential was -0.5 kPa, but supplemented with PEG-8000 to set a matric potential equivalent of -0.5 or -1.0 MPa. Incubations were again 5 days. In addition, we tested the effect of gas pressure on gene expression profile of cells in liquid medium. 20 ml of overnight grown KT2440 cells were exposed to 0.4 MPa (gauge) and 0.1 MPa (atmospheric) pressures. Matric Stress Experiments: we had 3 to 4 replicates for each time point and controls (-0.5 kPa). These were kept under -0.4 MPa stress at 4 hr (P4), 24 hr (P24), 72 hr (P72), and controls kept at -0.5 kPa (C).

2010-11-24 | E-GEOD-25512 | biostudies-arrayexpress

differential gene expression dynamics of Pseudomonas putida KT2440 under matric stress

2010-11-24 | GSE25512 | GEO

dreb1a expression data from Arabidopsis flowers under drought stress

Project description:We used microarray analysis to examine transcriptomic changes upon dreb1a under drought, identifying hundreds of genes that potentially function downstream of DREB1A and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. DREB1a mutant (CS872453) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.

2013-11-06 | E-GEOD-43724 | biostudies-arrayexpress

Expression data from Arabidopsis flowers under drought stress

Project description:We also used microarray analysis to examine transcriptomic changes under drought, identifying thousands of genes that potentially mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

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