Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-14374
PROVIDER: PRJNA111417 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds. Experiment Overall Design: Col-0 and pil5 seeds were irradiated by far-red light or far-red/red light and then, incubated in the dark for 12 hours. Total three biological replicates were used for the microarray.
2010-01-19 | E-GEOD-14374 | biostudies-arrayexpress
Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of imbibed Arabidopsis thaliana Columbia-0 ecotype seeds that were treated with a 20 min red or far red pulse. The red-light pulse induces germination.
2019-07-10 | GSE134019 | GEO
Project description:Transcriptional profiling of Arabidopsis far-red light pulse treated seeds comparing luh mutant with wild type (Col-0). Seeds were imbibed within 1 hr under white light and treated far-red light pulse for 5 min followed by 12 hr dark incubation. Goal was to determine the effects of LUH as transcriptional co-regulator during seed germination process.
2015-09-27 | GSE70406 | GEO
Project description:There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates. For 12 organs, three lines of plants were grown in soil under the long-day conditions of 16 hours light at 22℃. Samples were collected from each of juvenile rosette leaves, adult rosette leaves, cauline leaves, stems, young flower buds (sepals were closed and petals are not visible), mature flower buds (petals are visible), flowers, young siliques filled with white seeds, mature siliques filled with green seeds, old yellowing siliques (2-month-old) and senescence rosettes. Root tissues were collected from 2-week-old plants growing on 1% agar plates containing Murashige and Skoog (MS). Callus were collected from cultured CIM (callus induction medium) containing B5 medium supplemented with 20 g liter–1 glucose, 0.5 mg liter–1 2,4-D, and 0.1 mg liter–1 kinetin. Dry seed was defined to be after-ripened seeds for 4 weeks. Imbibed seeds are collected from seeds imbibed on the moistened paper for 24 and 48 hours under the continuous light at 22℃. In light irradiations, wild type (WT) seeds were plated on MS plates. For the time course experiment of white light, the plates were placed at 4°C in darkness for at least 2 days prior to receiving 6 h red light irradiation to synchronize germination. Then, plates were placed in the dark for 3 days and then exposed to white fluorescent light (100 μmol m–2 s–1) for 1, 6 and 24 h. For monochromatic light experiment, WT seedlings were grown in continuous red light, blue light, far-red light, or darkness for 6 days after red light irradiation. The light intensity used was 0.17 μmol m–2 s–1 for red light, 1.16 μmol m–2 s–1 for blue light and 0.53 μmol m–2 s–1 for far-red light. All abiotic stress samplings were collected from plants grown for 2 weeks on MS plates under 2 and 6 hours of abiotic stress conditions at the continuous light at 22℃. For drought stress treatment, plants were transferred and dehydrated onto the dried filter paper in the covered plastic dishes. For heat and cold stress treatments, the covered plastic dishes with plants were transferred directly from 22 to 37 and 2℃ respectively. For salinity stress treatment, plants were transferred onto the filter paper moistened with MS plates including 200mM NaCl.
2012-09-30 | E-GEOD-34188 | biostudies-arrayexpress
Project description:There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates.
2012-09-30 | GSE34188 | GEO
Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds. Keywords: genetic modification
2010-01-12 | GSE14374 | GEO
Project description:To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT) Seeds of No-0 WT, 35S::pBVR3 and CAB3::pBVR2 on MS plates were exposed to Red (R) light of 75 M-BM-5mol m-2 s-1 for 5 min and imbibing seeds were cold-stratified at 4 M-BM-0C in darkness for 3 d. Seedlings were grown under continuous far-red illumination for 7 d. Seven-day-old vegetative whole seedlings (300 M-bM-^@M-^S 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber. Seedlings were grown under continuous far-red illumination for 7 d.
2013-03-01 | E-GEOD-38989 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.
2017-08-10 | GSE85883 | GEO
Project description:To understand how GA functions in regulating embryo development, a genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of dellaq (rga28 gai rgl1 rgl2) and the wild-type (col-0-2) grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark). Then we found that GA regulates embryo development via DELLA-LEC1interaction, a subsequent genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of lec1-4 and the wild-type (col-0-1) in the same growth condition. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in dellaq vs col-0-2, lec1-4 vs Col-0-1 subsets, which are referred to as DELLA and LEC1 regulated genes. These data reveal that DELLAs and LEC1 co-target a set of common genes in late embryogenesis, strongly supporting the role of DELLA-LEC1 in embryo development.
2018-02-15 | GSE108544 | GEO
Project description:Arabidopsis thaliana ecotypes Columbia (Col-0) (wild type: WT) was used in this study. After sterilization, the seeds were placed on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22°C) / 8 hours dark (18°C) period in growth chamber at a light intensity of 120?150 µmol m-2 s-1. 20-day-old Arabidopsis leaves without bolting were immediately frozen in liquid nitrogen for RNA and protein and metabolites extraction. Leaves were harvested at three different time points: t = 0 hr (end of night), t = 1 hr (one hour after light turn on) and t = 8 hr (eight hours after light turn on), respectively.
2016-01-20 | GSE57791 | GEO