Transgenic GS1a poplar under different nitrate nutrition level.
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus tremula x Populus alba
SUBMITTER: Rafael Cañas
PROVIDER: E-GEOD-62449 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional profile of leaves from poplar plants transformed with a pine GS1a gene under two different nitrate nutrition level (50mM and 10mM).
2015-04-02 | GSE62449 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE16417: Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-overexpressor; GSE16419: Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-RNAi Experiment Overall Design: Refer to individual Series
2009-08-09 | E-GEOD-16420 | biostudies-arrayexpress
Project description:The transcriptome of Melampsora larici-populina was analysed in telia (in planta sample, early telia harvested before overwintering), uredinia (in planta sample, 168 hours post-inoculation, hpi), in planta during biotrophic growth (96 hpi) and in resting urediniospores. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to determine gene expression in early telia formed in decaying poplar leaves in autumn before the overwintering process and to compare this expression with other stages of the poplar rust life cycle that were previously described (i.e., resting urediniospores as pure fungal material, and uredinia and biotrophic growth stage as poplar leaf infecting fungal structures). This study should highlight telia-specific transcripts and contribute to the understanding of the poplar rust biological cycle. We performed 12 hybridizations (NimbleGen) with samples derived from resting urediniospores (3 biological replicates), infected poplar leaves harvested at 96 and 168 hpi (3 biological replicates each) and Telia (3 biological replicates). All samples were labeled with Cy3.
2013-11-01 | E-GEOD-49099 | biostudies-arrayexpress
Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization to Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the WRKY23-overexpressor plants were processed separately from the data for the Mmt-inoculated WRKY23-RNAi plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Experiment Overall Design: This part of the study includes 12 RNA samples consisting of three biological replicates for each of the mock-inoculated or Mmt-inoculated WT and WRKY23-overexpressing plants.
2009-08-09 | E-GEOD-16417 | biostudies-arrayexpress
Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization on Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the Mmt-inoculated WRKY23-RNAi plants were processed separately from the data for the WRKY23-overexpressor plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Normalized data for the Mmt-inoculated wildtype plants that were processed with the Mmt-inoculated WRKY23-RNAi plants are denoted with an "a" suffix. Experiment Overall Design: This part of the study includes 6 RNA samples consisting of three biological replicates for the Mmt-inoculated WT and WRKY23-RNAi (underexpressing) plants.
2009-08-09 | E-GEOD-16419 | biostudies-arrayexpress
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison
2011-09-29 | E-GEOD-27063 | biostudies-arrayexpress
Project description:Young poplar stems show a preponderantly primary growth in the top internodes and differential cambium activity in the basal internodes after inclination with some tension wood formed after 45 min. This study was conducted in order to characterize the early changes in gene expression during early stages of the gravitropic response in the poplar. Hybridizations were performed to compare gravistimulated poplar stems (basal region) after 45 min of inclination and untreated control stems. Two biological replicates were done. Two hybridizations with a dye swap for each tree pair were done, making a total of four hybridizations.
2013-04-12 | E-GEOD-44981 | biostudies-arrayexpress
Project description:Transgenic GS1a poplar under different nitrate nutrition level.
| PRJNA264146 | ENA
Project description:Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition. Our goal was to compare the transcriptomes of nitrate-supplied and ammonium-supplied plants, with a particular interest in characterizing the differences in redox metabolism elicited by different forms of inorganic nitrogen. We used microarrays to compare the short-term transcriptional response to either nitrogen supply or ammonium supply in Arabidopsis roots. Genes upregulated or downregulated by nitrate only, ammonium only, or both ammonium and nitrate were identified and analyzed. Arabidopsis thaliana (Col-0) plants were grown hydroponically until they reached growth stage 5.10. They were then transferred to a nitrogen-free medium for 26 hr and then supplied with 1 mM nitrate or 1 mM ammonium. RNA isolation (and subsequent microarray analysis) was performed on root tissue isolated just before nitrogen supply (time 0) and at 1.5 hr and 8 hr after nitrogen supply (1.5 hr nitrate, 8 hr nitrate, 1.5 hr ammonium, 8 hr ammonium).
2011-05-28 | E-GEOD-29589 | biostudies-arrayexpress
Project description:Simulating predicted future climate conditions, stress response and stress-related memory after one week of recovery were transcriptionally characterised in young and old leaves, phloem-bark, developing xylem and roots of 3-month-old Grey poplar plants that had undergone three weeks of stress or were kept under control conditions. The control conditions include ambient or elevated CO2 levels (380 μL L-1 and 500 μL L-1, respectively) with a daily maximum temperature of 27 °C. The stress conditions include a periodic and a chronic drought-heat scenario at elevated CO2 levels (500 μL L-1) with a daily maximum temperature of 33 °C. The periodic stress treatment included three cycles of reduced irrigation (50%, 60% and 70% reduction compared with the controls), each one lasting for six days; between the cycles, there were recovery periods with a duration of two days and a daily maximum temperature of 27 °C. In the chronic stress treatment, irrigation was gradually reduced for 22 days, down to 70% reduction compared with the controls. Three biological replicates were examined per group defined by a specific environmental condition (droughtPER: periodic stress, droughtCHR: chronic stress, control500: elevated CO2 control, control380: ambient CO2 control), a specific harvesting time (S: stress phase, R: recovery phase) and a specific tissue (LE1: young leaves, LE2: old leaves, PHL: phloem-bark, XYL: developing xylem, ROO: roots). For stress phase ambient CO2 control in old leaves, one replicate failed quality control.
2019-01-11 | E-MTAB-6121 | biostudies-arrayexpress