Transcription profiling of Arabidopsis wild type and ARB17-over-expressing plants
Ontology highlight
ABSTRACT:
INSTRUMENT(S): arrayWoRx Biochip Reader [Applied Precision]
ORGANISM(S): Arabidopsis thaliana
DISEASE(S): not applicable
SUBMITTER: Nat Kav
PROVIDER: E-MEXP-1024 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The investigation contains two sets of experiment. Set I. Transcriptional profiling of salt treated WT A. thaliana (WS ecotype) (100mM NaCl WT/0mM NaCl WT): Set II. Transcriptional profiling of salt treated ABR17- A. thaliana lines (100mM NaCl ABR17/0mM NaCl ABR17). <br>Tissue for microarray analysis was obtained by placing surface sterilized seeds of A. thaliana (line 6.9) and the WT on half strength Murashige & Skoog (MS)(Murashige and Skoog, 1962) medium (1.5% sucrose, 0.8% agar with pH 5.7) medium in Petri dishes with or without 100mM NaCl at RT (21 ± 2 °C) after surface sterilization. The seeds were surface sterilized by rinsing with 70% ethanol for one minute, incubation in 20% bleach for 15 min and subsequent washes (four times for 5min each) to remove the bleach. MS plates with the seeds were placed at RT (21 ± 2 °C) under continuous fluorescent light 30 ?mol m-2 s-1 for 14 days. Seedlings (14 day-old) from three independently grown biological replicates in two set of experiments were removed from the MS plates, flash frozen in liquid nitrogen and stored at 80 °C until used for RNA extraction.<br>Technical protocols for preparing the hybridization extract:<br><br>1. RNA was isolated using the QIAGEN RNeasy Plant Mini Kit (Qiagen Inc., Mississauga, ON, Canada) from two-week-old WT (grown on 0 and 100mMNaCl) and ABR17 (grown on 0 and 100mMNaCl) seedling tissue grown at three independent times (biological replicates). The integrity of all RNA samples assessed by agarose gel (1.2 percent) electrophoresis. <br><br>2. 6 ?g (Six micrograms) of total RNA was used to synthesize cDNAs using SuperScript® II RT (Invitrogen Inc., Burlington, ON, Canada) with RT polyA-capture primers in 3D Array 900TM (Genisphere Inc., Hatfield, PA, USA). Each pair of treated (100mM NaCl) and untreated (0mM NaCl) samples within each of the three biological replicates from two sets of experiments (100mM NaCl WT/0mM NaCl WT ; 100mM NaCl ABR17/0mM NaCl ABR17) was labelled in a reciprocal dye-swap design, for a total of 12 hybridizations. <br><br><br>Note: In the transgenic plant production, the pea cDNA encoding for ABR17 was constitutively expressed under the control of Cauliflower mosaic virus 35S promoter. <br>Reference: Srivastava S., Rahman H., Shah S. and Kav N.N.V. Constitutive<br>expression of pea ABA-responsive 17 (ABR17) cDNA confers multiple<br>stress tolerance in Arabidopsis thaliana. Plant Biotechnology Journal<br>(2006) 4, 529-549.<br><br><br>
2009-04-04 | E-MEXP-1566 | biostudies-arrayexpress
Project description:Seeds of A. thaliana were sowed on culture medium poured in Magenta boxes. They were allowed to germinate. Plantlets were in vitro for 5 or 11 days and harvested for RNA extraction.
2007-07-17 | E-MEXP-789 | biostudies-arrayexpress
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2006-02-10 | E-MEXP-268 | biostudies-arrayexpress
Project description:Growth in the presence of sucrose was shown to confer to Arabidopsis thaliana seedlings, under conditions of in vitro culture, a very high level of tolerance to the herbicide atrazine and to other photosynthesis inhibitors (Sulmon et al., 2004). The CATMA investigation will be useful to reveal the gene networks implicated in the mechanisms of xenobiotics tolerance. Seeds of Arabidopsis thaliana (ecotype Columbia) were surface-sterilized inbayrochlore/ethanol (1:1, v/v), rinsed in absolute ethanol and dried overnight. Germination and growth were carried out under axenic conditions in square Petri dishes. After seeds were sowed, Petri dishes were placed at 4 C for 48 h in order to break dormancy and homogenize germination, and then transferred to a control growth chamber at 22°C under a 16-h light period regime at 4500 lux for 4 weeks. Growth medium consisted of 0.8% (w/v) agar in 1x Murashige and Skoog (MS) basal salt mix (Sigma, St. Louis, MO, USA) adjusted to pH 5.7. After 4 weeks of cultivation on vertical plates plantlets were transferred on fresh medium complemented or not with atrazine 10 uM and with sucrose 80mM or mannitol 80 mM which were directly added during preparation of agar-MS media prior to sterilisation. Atrazine was sterilized by microfiltration through 0.2 um cellulose acetate filters (Polylabo, Strasbourg, France) and then axenically added to melted agar-MS medium prior to pouring into Petri dishes. Then plantlets were harvested after 24 hours of transfer and extracted for RNA.
2006-08-23 | E-MEXP-411 | biostudies-arrayexpress
Project description:Experiment 1<br> Gene profiling upon biotic stress treatment<br> Biological question : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment?<br> Experiment description : 14-day old seedlings (Col-0 and fls2 KO) treated with 10uM of flg22 (flagellin- derived peptide) over a one hour timecourse.<br> <br> Experiment 2<br> Gene profiling in microRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants?<br> Experiment description : Ler, dcl1-9, hen1-1 and hasty were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 3<br> Gene profiling in siRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants?<br> Experiment description : Col-0, dcl2-1, dcl3-1 and rdr2-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 4<br> Gene profiling in Agrobacterium-induced tumors and auxin-induced calli.<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in an Agrobacterium-induced tumors compared to auxin-induced calli?<br> Experiment description : Col-0 plants were infected with wt Agrobacterium tumefaciens (strain A208) by stabbing the emerging stems. 18 days later, growing tumors were harvested as were the non-infected part of the stabbed-stem.In parallel, Col-0 seeds were germinated on Callus Induction Media (CIM) and 18 days later, calli were harvested.<br> <br> Experiment 5<br> Gene profiling in tasiRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of tasiRNA mutants?<br> Experiment description : Col-0, dcl4-1, rdr6-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 6<br> Gene profiling upon biotic stress treatment<br> Biological question : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment?<br> Experiment description : 14-day old seedlings (Col-0 and fls2 KO) treated with 10uM of flg22 (flagellin- derived peptide) over a one hour timecourse.<br> <br> <br>
2006-12-20 | E-MEXP-517 | biostudies-arrayexpress
Project description:Seeds of Arabidopsis thaliana (ecotype Columbia) were surface-sterilized inbayrochlore/ethanol (1:1, v/v), rinsed in absolute ethanol and dried overnight. Germination and growth were carried out under axenic conditions in square Petri dishes. After seeds were sowed, Petri dishes were placed at 4°C for 48 h in order to break dormancy and homogenize germination, and then transferred to a control growth chamber at 22°C under a 16-h light period regime at 4500 lux for 4 weeks. Growth medium consisted of 0.8% (w/v) agar in 1x Murashige and Skoog (MS) basal salt mix (Sigma, St. Louis, MO, USA) adjusted to pH 5.7. After 4 weeks of cultivation on vertical plates plantlets were transferred on fresh medium complemented with atrazine 10 µM and with sucrose 80mM or mannitol 80 mM which were directly added during preparation of agar-MS media prior to sterilisation. Atrazine was sterilized by microfiltration through 0.2 µm cellulose acetate filters (Polylabo, Strasbourg, France) and then axenically added to melted agar-MS medium prior to pouring into Petri dishes. Then plantlets were harvested after 12, 24 and 48 hours of transfer and extracted for RNA. Plantlets grown on MS medium were harvested and extracted for RNA as control.
2007-03-10 | E-MEXP-574 | biostudies-arrayexpress
Project description:Comaprison of PBMCs from patients with systemic juvenile idiopathic arthritis during active and inactive disease
2007-03-31 | E-MEXP-987 | biostudies-arrayexpress
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2006-06-01 | E-MEXP-373 | biostudies-arrayexpress
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