Transcriptomics Analyses of tobacco leaves and roots sample during water-deficit
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ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE67434 | GEO | 2015/03/31
SECONDARY ACCESSION(S): PRJNA279897
REPOSITORIES: GEO
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Project description:Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblegen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons. The seeds were sown in sterile petri plates with modified half-strength MS agar medium. The seedlings were then aseptically transferred into sterile polycarbonate container with half-strength MS liquid medium. Seedlings were grown for 2 weeks in an incubator set at 25 oC with constant light and subjected to dehydration for 20min, 40min, 1hr, 2hrs, and 4hrs. We used a hydrophonics system for the trancriptome profiling of tobacco (cv Burley 21) root and leaves samples to study plant reponses during water- deficit or drought. Plants were grown in controlled growth chamber conditions and subjected to water deficit condition after 2 weeks.The plants were transferred to empty containers without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tissues and hence called 0-min dehydrated tissue. Similarly other time-points were processed( for instance, 20 min of dehydration, plants were dehydrated for 20 min after being taken out from the container and then harvested). Tissues for three biological replicates and 20 plants per biological replicates were collected for each time-point. RNA was isolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.
2015-03-31 | E-GEOD-67434 | biostudies-arrayexpress
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2014-02-07 | E-MEXP-3827 | biostudies-arrayexpress
Project description:Arabidopsis wild type and atglr3.3 mutant seedlings were cultured on 0.7% (w/v) agar medium containing half strength of MS basic salt with 1% sucrose (w/v), 5mM MES, pH 5.7. 10-day-old seedlings were equilibrated in the CK buffer for 24 hours. Then, these seedlings were either treated with the CK buffer or the CK buffer containing 100 ?M GSH and 100 ?M Glu for 1 hour, respectively.
2013-09-30 | E-MEXP-3885 | biostudies-arrayexpress
Project description:Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hours Keywords: repeat sample
2004-08-31 | GSE862 | GEO
Project description:Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h. Experiment Overall Design: Arabidopsis thaliana ecotype Columbia glabra (gl1-1) was used in this study. Seeds were sterilized with diluted bleach (10 min incubation in 1.7% sodium hypochlorite, rinsing and washing thoroughly in sterile water), and incubated in 2.5 ml liquid growing medium [Murashige-Skoog (MS) half strength solution] in 6-well plates (fully aerobic, with shaking). Plates were incubated in the darkness at 4°C for 2 days and finally transferred to 23°C for 4 days before the sugar treatments (with 90 mM sucrose, lasting 6h). Two independent, replicated experiments were performed for sucrose treatments. Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction. Experiment Overall Design: AIR EXPERIMENT 1: Control without added sucrose Experiment Overall Design: AIR EXPERIMENT 2: Control without added sucrose Experiment Overall Design: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 1 Experiment Overall Design: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 2
2008-06-12 | E-GEOD-3704 | biostudies-arrayexpress
Project description:The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column. Experimenter name = Martin Broadley Experimenter phone = 0115 951 6382 Experimenter fax = 0115 951 6334 Experimenter institute = University of Nottingham Experimenter address = Plant Sciences Division Experimenter address = School of Biosciences Experimenter address = University of Nottingham Experimenter address = Sutton Bonington Experimenter address = Loughborough Experimenter zip/postal_code = LE12 5RD Experimenter country = UK Keywords: growth_condition_design
2007-01-08 | GSE5614 | GEO
Project description:Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hours
2007-07-10 | E-GEOD-862 | biostudies-arrayexpress
Project description:The purpose of the experiments is to understand transcriptional reprogramming in roots of halophyte Schrenkiella parvula (S. parvula) that may contribute to its high salt tolerance. Root materials were harvested from S. parvula seedlings grown on agar plates with ½ strength Murashige-Skoog (½MS) medium including vitamins for 4 days and transferred to ½MS medium supplemented with 0mM or 175mM NaCl for 0h, 3h, 24h or 48h.
2023-02-18 | E-MTAB-12424 | biostudies-arrayexpress
Project description:Barley1 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). Eight day old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)3) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Surface sterilized seeds were aseptically germinated and grown on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days at 23±2ºC with 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle with 70% relative humidity. Seedlings were transferred to sterile hydroponic cultures for B treatment, which was applied immediately after transfer as half strength Hoagland’s solution containing either 5 mM B(OH)3 (5B) or 10 mM B(OH)3 (10B) for another 5 days under the same physical conditions. Control (C) groups were transferred to half strength Hoagland’s solution without extra B(OH)3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Mehmet Tufan OZ. The equivalent experiment is BB63 at PLEXdb.]
2009-01-24 | GSE14521 | GEO
Project description:We treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis (GeneChip microarrays) in order to identify genes and transcription factors regulated by chitosan. The results showed that jasmonate and defense responsive genes, camalexin and lignin biosynthetic genes were among genes up-regulated by chitosan. Several transcription factors are also strongly induced by chitosan. The results suggested that chitosan can be used as a strong elicitor of defense pathways. Experiment Overall Design: Arabidopsis thaliana, ecotype Columbia (Col-0) seeds were sterilized for 7 min in 1.7% (v/v) bleach solution, incubated over night in 4% PPM (Plant Preservative Mixture, Plant Cell Technology, Washington DC, USA) in a full strength sterilized Murashige-Skoog (MS) salt solution with gentle shaking. Subsequently, the seeds were rinsed in abundant sterile water and transferred into 2.5 ml liquid growing media (MS half strength solution) with 0.05% PPM in 6-well plates. The plates were incubated in the dark at 4 °C for two days and finally transferred to continuous light (90µm photons/ m-2) with gentle swirling for four days in a plant growth chamber at 22 °C. Experiment Overall Design: . Treatments were performed by comparing a control solution containing the solvent used to solubilize chitosan, and a chitosan solution concentrated 150 µg/ml.
2009-11-10 | E-GEOD-17193 | biostudies-arrayexpress