Transcriptional responses to dark induced senescence in Nicotiana tabacum.
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana tabacum
SUBMITTER: Kieron Edwards
PROVIDER: E-MTAB-602 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:A study was carried out to compare gene expression levels between technical replicate samples in order to test the reproducibility of a custom Affymetrix microarray for Tobacco (Nicotiana tabacum).
2009-01-01 | E-MTAB-72 | biostudies-arrayexpress
Project description:Gene expression was measured in different tissues throughout the lifecycle of the Nicotiana tabacum plant to generate the Tobacco Expression Atlas (TobEA).
2009-12-05 | E-MTAB-176 | biostudies-arrayexpress
Project description:Although significant work has been undertaken regarding the response of model and crop plants to heat shock during the acclimatory phase, few studies have examined the steady state response to the mild heat stress encountered in temperate agriculture. In the present work we therefore exposed tuberising potato plants to mildly elevated temperatures (30/20C), day/night) for up to five weeks and compared tuber yield, physiological and biochemical responses, and leaf and tuber metabolomes and transcriptomes with plants grown under optimal conditions (22/16C). Growth at elevated temperature reduced tuber yield despite an increase in net foliar photosynthesis. This was associated with major shifts in leaf and tuber metabolite profiles, a significant decrease in leaf glutathione redox state and decreased starch synthesis in tubers. Furthermore, growth at elevated temperature had a profound impact on leaf and tuber transcript expression with large numbers of transcripts displaying a rhythmic oscillation at the higher growth temperature. RT-PCR revealed perturbation in the expression of circadian clock transcripts including StSP6A, previously identified as a tuberisation signal. Our data indicate that potato plants grown at moderately elevated temperatures do not exhibit classic symptoms of abiotic stress but that tuber development responds via a diversity of biochemical and molecular signals. In this submission we are looking at gene expression changes with respect to both temperature and time, every 4h over a 24h period whereby diurnal changes may be apparent.
2013-08-01 | E-MTAB-1655 | biostudies-arrayexpress
Project description:Arabidopsis HMA4 transformation facilitates Zn root-to-shoot translocation, but in Zn-supply dependent manner. It implies that distinct effects of HMA4 expression on Zn root:shoot distribution in transgenics grown under different Zn supply regimes results from the interaction between the transgene activity and the molecular background of the host plant. Microarray analysis was performed to compare expression profiles in leaves of transgenic and WT-plants grown in the presence of 5 µM Zn to identify the molecular mechanism underlying the difference in Zn root:shoot distribution between 35S:AtHMA4-expressing and wild-type tomato. To recognize tissue specific alterations in gene transcription in tomato leaves invoked by AtHMA4 expression, spongy paerenchyma + lower epidermis and palisade paerenchyma + upper epidermis were isolated using LCM technique. Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose. 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment the 3rd and 4th leaf (counting upwards) were collected, 1-2 mm long and 2-3 mm wide fragments were cut out from between the vascular bundles in the middle part of each leaf, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of leaves was amplified and used for three independent microarray analysis.
2015-05-08 | E-GEOD-68640 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-05-08 | E-GEOD-68641 | biostudies-arrayexpress
Project description:Ectopic expression of AtHMA4 in tomato modified Zn accumulation in a Zn-supply dependent manner. It suggests that HMA4-expression under a range of Zn-supply differentially modifies the expression of endogens, which contributes to different Zn-related phenotypes. To identify genes differentially regulated in 35S:AtHMA4-expressing and wild-type tomato, the transcription profiles were compared between roots of transgenic and WT-plants grown in the presence of 5 µM Zn. An effort was undertaken to recognize tissue specific alterations underlying the difference in Zn root:shoot distribution between tested plant lines and LCM technique was used to isolate epidermis+cortex and stele from roots.Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose. 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment 2.0 cm long root fragments from six plants (excluding 1.5 cm long apical fragments) were pooled, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of roots was amplified and used for three independent microarray analysis.
2015-05-08 | E-GEOD-68639 | biostudies-arrayexpress
Project description:We created a gene expression atlas of major organs and under environmental perturbations (temperature and light) of the lycophyte Selaginella moellendorffii
2020-01-21 | E-MTAB-8217 | 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:Yield losses as a result of abiotic stress factors present a significant challenge for the future of global food production. While breeding technologies provide potential to combat negative stress-mediated outcomes over time, interventions which act to prime plant tolerance to stress, via the use of phytohormone-based elicitors for example, could act as a valuable tool for crop protection. However, the translation of fundamental biology into functioning solution is often constrained by knowledge-gaps. Photosynthetic and transcriptomic responses were characterised in young tomato (Solanum lycopersicum) seedlings in response to pre-treatment with a new plant health activator technology, M-bM-^@M-^XAlethea,M-bM-^@M-^Y followed by a subsequent 100 mM salinity stress. Salinity treatment led to a maximal 47% reduction in net photosynthetic rate 8 d following NaCl treatment. In Alethea pre-treated seedlings, sensitivity to salinity stress was markedly reduced during the experimental period. Microarray analysis of leaf transcriptional responses showed that while salinity stress and Alethea individually impacted on largely non-overlapping, distinct groups of genes, Alethea pre-treatment substantially modified the response to salinity. Alethea affected the expression of genes related to biotic stress, ethylene signalling, cell wall synthesis, redox signalling and photosynthetic processes. Since Alethea had clear effects on photosynthesis/chloroplastic function at the physiological and molecular levels, we also investigated the ability of Alethea to protect plants against methyl viologen, a potent generator of oxidative stress in chloroplasts. Alethea pre-treatment produced dramatic reductions in visible foliar necrosis caused by methyl viologen compared with non-primed controls. Tomato leaves from four groups of treated plants were harvested at a single point following treatment for RNA extraction and hybridization on Affymetrix microarrays. Plants came from two initial groups, pre-treated either with water (control) or the Alethea product. Equal numbers of plants from within these groups were subsequently treated either with water (control) or salinity (100 mM NaCl), generating 4 main experimental groups in a 2x2 factorial design. Samples were collected from 3 biological replicate experiments, and each sample included leaves pooled from 3 individual plants from each treatment group.
2013-01-15 | E-GEOD-43492 | biostudies-arrayexpress
Project description:Comparison of Arabidopsis genotypes Col-0 and C24 grown in controlled environment conditions
2010-07-30 | E-MEXP-2732 | biostudies-arrayexpress