Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage
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PROVIDER: PRJNA248379 | ENA |
REPOSITORIES: ENA
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Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2014-10-15 | GSE57895 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed
2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2016-06-30 | GSE76613 | GEO
Project description:Proteomics analyses of roots and shoots of O. sativa plants exposed to cold stress.
2022-02-16 | PXD028712 | Pride
Project description:Arabidopsis Col-0 seedlings grown in liquid culture to growth stage 1.0 were treated with 5 M-5M Benzyladenine and incubated for the indicated time points. Roots and shoots of the seedlings were then harvested separately by taking each individual seedling with a soft forceps at the hypocotyl, dipping it into liquid nitrogen and breaking off the root at the inner wall of a collection tube that was swimming in liquid nitrogen. The shoot part was then striped from the forceps at the edge of another collection tubes.
2011-06-20 | E-CAGE-111 | biostudies-arrayexpress
Project description:The root-colonizing endophytic fungus Piriformospora indica promotes root and shoot growth of its host plants. We show that growth promotion of Arabidopsis leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more label can be detected in the leaves of N-starved host plants, but not of plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host to the N limitation condition. P. indica alters the expression of transporter genes which participate in relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant´s metabolomic adaptation to N limitation by delivering reduced N metabolites to the host, alleviating metabolic N starvation responses, and reprogramming the expression of N-metabolism related genes.
2023-10-19 | GSE239281 | GEO
Project description:Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction. We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the downregulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance. Twelve day-old (48 h cold treatment and 10 days of illumination) Arabidopsis seedlings of equal sizes were selected for co-cultivation experiments. They were transferred to PNM plates with a nylone membrane on the top (Johnson et al. 2011) and exposed to a fungal plug 5 mm in diameter or a KM plug of the same size without fungal hyphae (control). The plugs were placed 3 cm away from the closest root part . The light intensity (80 ± 5 μmol m-2 sec-1) was checked every third day to ensure that both P. indica- and mock-treated seedlings receive equal amounts of light.
2016-05-30 | E-GEOD-58771 | biostudies-arrayexpress
Project description:This experiment was designed to identify transcribed regions of indica rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogate the indica genome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: genome tiling experiments
2005-10-15 | GSE3452 | GEO
Project description:Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression. The seedlings were grown on MS medium with 1.37% sucrose under short day conditions and low light intensity (30 µmol m-2s-1) at 20˚C for 14 days. Transcriptome analysis was performed for the rrtf1 knock-out line and a RRTF1-overlexpressor line (called oe18) in comparison to wild-type seedlings.
2015-04-23 | E-GEOD-64783 | biostudies-arrayexpress