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Expression profile of Arabidopsis thaliana seedlings subjected to hypoxia

ABSTRACT: Arabidopsis thaliana (Col-0) seedlings were grown on vertically oriented agar plates and subjected to hypoxia (0.2% oxygen, 99.8% nitrogen) for 30 to 240 minutes.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE60133 | GEO | 2014/08/07

SECONDARY ACCESSION(S): PRJNA257548

REPOSITORIES: GEO

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Expression profile of Arabidopsis thaliana seedlings subjected to hypoxia

Project description:Arabidopsis thaliana (Col-0) seedlings were grown on vertically oriented agar plates and subjected to hypoxia (0.2% oxygen, 99.8% nitrogen) for 30 to 240 minutes. Five independent samples were analysed: three samples were subjected to hypoxia treatment and two samples were kept at ambient conditions;

2014-08-07 | E-GEOD-60133 | biostudies-arrayexpress

Microarray hybridization data from the root tips of 5-day-old Arabidopsis thaliana seedlings grown on tilted, hard agar surfaces

Project description:The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion. Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting. The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment. Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates. Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one. We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2. This line has an intermediate skew between its two parents.

2011-03-31 | GSE28275 | GEO

Expression data from wildtype and spy-3 roots

Project description:SPY is an O-linked N-acetylglucosamine transferase involved in many signaling and developmental processes in Arabidopsis. SPY also has a role in root development. In the spy mutant, a middle cortex is produced prematurely. To understand how SPY regulates root cortex proliferation, we sought to identify the genes affected by the spy mutation in the root. The transciptomes from the root of one-week-old seedlings, Col or spy-3 mutant, were compared. The seedlings were grown on a nylon membrane placed on 1X MS agar medium and the plates are positionally vertically in a Pecival growth chamber with 16 hr light and 8 hr dark. Three biological replicates were performed.

2015-05-16 | E-GEOD-50952 | biostudies-arrayexpress

Microarray hybridization data from the root tips of 5-day-old Arabidopsis thaliana seedlings grown on tilted, hard agar surfaces

2011-03-31 | E-GEOD-28275 | biostudies-arrayexpress

Transcription profiling of Arabidopsis 3 day-old seedlings of acn1-2 and the parent, Col-7 in the presence/absence of sucrose

Project description:Arabidopsis acetate non-utilizing mutants were isolated based on fluoroacetate resistant germination. Interestingly, a number of these mutants exhibited altered developmental characteristics in response to exogenous sucrose supply, such as bleaching of the cotyledons. A preliminary microarray experiment has already been conducted on one of the mutants, acn1-2. The gene expression analysis was done using 3 day-old seedlings of acn1-2 and the parent, Col-7, which were germinated on agar plates with and without exogenous sucrose. A cross-comparison of acn1-2 and Col-7 revealed that the expression of a number of carbohydrate responsive genes was altered in the mutant. The request for further microarray analysis is to confirm this result.

2022-11-21 | E-NASC-29 | biostudies-arrayexpress

Differential gene expression in seedlings of pi4kb1b2-Study of pi4kb1b2 mutant

Project description:ngs2020_14_pi4kb1b2-differential gene expression in seedlings of pi4kb1b2-Differential gene expression in roots and leaves of seedlings, pi4kb1b2 mutant vs WT-Comparison of gene expression profile between roots and leaves of A.thaliana Col-0 as WT and pi4kb1b2 mutant, 7 days old (developmental stage 1.02), cultivated on MS/2 media supplemented with 0.8% agar and 1% sucrose, 22°C, 16h/8h light)

2022-05-04 | GSE179635 | GEO

Gene expression profiling of laser-captured microdissected avascular neocortex in E14.5 neocortical cells were compared by microarray transcription profiling

Project description:Gene expression profiles among avascular region (around ventricular zone), highly vascularized region with honeycomb-patterned vascular plexus (around subventricular zone and intermediate zone), and cortical plate with vertically oriented vessels from laser-captured microdissected E14.5 neocortex were compared by microarray

2019-09-18 | E-MTAB-8359 | biostudies-arrayexpress

Gene expression profile in root and flower mediated by GLUCOSE-INHIBITED ROOT ELONGATION1 (GIR1)

Project description:We isolated the glucose-inhibited root elongation1 (gir1) mutant from a genetic screen of activation T-DNA tagged seeds grown on 6% glucose agar plates. The gir1 mutant showed short swollen root phenotype at the presence of glucose and had a sever sterility when grown in soil. To better understand the molecular basis of GIR1-mediated gene expression, the Affymetrix ATH1 GeneChip was used to analyze the gene expression profiling in the gir1 mutant. The results showed that cell wall, carbohydrate, and lipid metabolic or transporter-related genes were altered expression pattern. These data suggest that GIR1 regulates root and flower growth and development through cell wall modification and, perhaps, membrane trafficking. For root microarray assay [Samples GSM402178-GSM402183], wild type and the gir1 mutant plants were vertically grown on 0% glucose agar plates for 11 days, then transferred to 4% glucose plates for another ten days. Subsequently, the root tissues were excised for GeneChip analysis. In the case of inflorescence microarray assay [Samples GSM402184-GSM402191], plants were grown in soil for 33 days. The opened and opening flowers were discarded and the remaining inflorescence was harvested for GeneChip analysis.

2010-07-30 | E-GEOD-16056 | biostudies-arrayexpress

Effect of NJ15 on gene expression profiles in Arabidopsis thaliana seedlings

Project description:Brassinosteroid (BR) and auxin co-regulate plant growth in a process termed cross-talking. Based on the assumption that their signal transductions are partially shared, inhibitory chemicals for both signal transductions were screened from a commercially-available library. A chemical designated as NJ15 (ethyl 2-[5-(3,5-dichlorophenyl)-1,2,3,4-tetrazole-2-yl]acetate) diminished the growth promotion of both adzuki bean epicotyls and Arabidopsis seedlings, by either the application of BR or auxin. To understand its target site(s), bioassays with a high dependence on either the signal transduction of BR (BR-signaling) or of auxin (AX-signaling), were performed. NJ15 inhibited photomorphogenesis of Arabidopsis seedlings grown in the dark, which mainly depends on BR-signaling, while NJ15 also inhibited their gravitropic responses mainly depending on AX-signaling. On the study for the structure-activity relationships of NJ15 analogues, they showed strong correlations on the inhibitory profiles between BR- and AX-signalings. These correlations imply that NJ15 targets the downstream pathway after the integration of BR- and AX-signals. Arabidopsis thaliana ecotype Col-0 was used as the wild type (WT) in this study. The Col-0 plants, grown vertically as a gravitropic response assay for 4 days on MS plates, were sprayed with mock or with 10 µM NJ15 (ethyl 2-[5-(3,5-dichlorophenyl)-1,2,3,4-tetrazole-2-yl]acetate) and were gravistimulated by turning then 90° relative to the first direction. After 8 h, plants were harvested and total RNA was extracted with a Total RNA Extraction Kit Mini for plant (RBC Bioscience), then total RNA was subjected to microarray analysis.

2014-11-03 | E-GEOD-57449 | biostudies-arrayexpress

Transcription profiling of Arabidopsis XW119 seedlings 0-4 hours after ethanol induction

Project description:4-day-old XW119 seedlings were treated with 2% Ethanol on MS agar plates under light, and samples were collected at 0, 1, 2, 4 hours.

2010-04-19 | E-MEXP-2229 | biostudies-arrayexpress

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