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ABSTRACT:
PROVIDER: PRJNA1012728 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:This SuperSeries is composed of the following subset Series: GSE30711: ChIP-Seq data from Arabidopsis thaliana under dark and far-red light GSE30712: Expression data from Arabidopsis thaliana under dark and far-red light Refer to individual Series
2011-12-31 | E-GEOD-30713 | biostudies-arrayexpress
Project description:Arabidopsis thaliana wildtype (Col-0) was compared with the ntrc mutant under different photoperiods (short day: 8h/16h; long day 16h/8h light/dark) and different ages (10d and 28/21d).
2009-06-02 | E-MEXP-1697 | biostudies-arrayexpress
Project description:ngs2015_01_transition-transition-Identification of transcripts and long non-coding transcripts in wild-type mature rosette leaves of Arabidopsis thaliana during a photoperiodic switch inducing floral transition.-Arabidopsis thaliana Col-0 plants were grown in soil, in growth chamber under white fluorescent light, under short-day (8 hours light/16 hours dark, SD) or long-day (16 hours light/8 hours dark, LD) conditions. Temperature in SD was 21°C during the light period and 18°C during the dark, humidity (65%) remained constant. In LD, temperature (21°C) and humidity (70%) remained constant. Plants were cultured for 4 weeks in individual pot, in SD then transferred in LD. Plants were analysed at different time points before transfer (T0) and after two, three and five days of transfer (T2, T3, T5). The second pair of leaves was collected before dusk, at Zeitgeber time 15 (ZT15) considering ZT 0 the switched on of the light. Three biological replicates were performed. The floral transition occurs between T0 and T5 based on AP1:GUS marker, a inflorescence meristem is not yet visible during this developmental window at the center of the rosette.
2019-04-17 | GSE116123 | 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
Project description:Transcriptional comparison of Arabidopsis thaliana pvip1;pvip2 RNAi double mutants against Col-0 wildtype. Tissue used: whole rosettes of 4-week-old plants grown under short-day conditions (8h light; 20oC). 3 biological replicates for each. Control = Col-0 and mutant = pvip1;pvip2. PVIP = Potyvirus-VPg-interacting protein (Dunoyer et al. 2004 J. Virol. 78: 2301-2309).
2009-12-11 | GSE19341 | GEO
Project description:micrarray profiling on Arabidopsis thaliana col-0, cry1 and hfr1 in response to dark and 1 h blue light treatment
2008-10-29 | E-MEXP-1784 | biostudies-arrayexpress
Project description:The cold acclimation process is regulated by many factors like ambient temperature, day length, light intensity, or hormonal status. Experiments with plants grown under different light-quality conditions indicate that the plant response to cold is also a light-quality-dependent process. Here, the role of light quality in the cold response was studied in one-month-old Arabidopsis thaliana (Col‐0) plants exposed for one week to 4 °C at short‐day conditions under white (100 and 20 μmol m‐2s‐1), blue or red (20 μmol m‐2s‐1) light conditions. An upregulated expression of CBF1, an inhibition of photosynthesis, and an increase in membrane damage showed that blue light enhanced the effect of low temperature. Interestingly, cold-treated plants under blue and red light showed only limited freezing tolerance compared to white light cold-treated plants. Next, the specificity of the light quality signal in cold response was evaluated in Arabidopsis accessions originating from different and contrasting latitudes. In all but one Arabidopsis accessions, blue light increased the effect of cold on photosynthetic parameters and electrolyte leakage. This effect was not found for Ws-0, which lacks functional CRY2 protein, indicating its role in the cold response. Proteomics data confirmed significant differences between red and blue light treated plants at low temperature and showed that the cold response is highly accession specific. In general, blue light increased mainly the cold-stress related proteins and red light induced higher expression of chloroplast-related proteins, which correlated with higher photosynthetic parameters in red light cold-treated plants. Altogether, our data suggest that light modulates two distinct mechanisms during the cold treatment - red light driven cell function maintaining program and blue light activated specific cold response. The importance of mutual complementarity of these mechanisms was demonstrated by significantly higher freezing tolerance of cold-treated plants under white light.
2022-06-14 | PXD033102 | Pride
Project description:This RNA-seq was designed to help gain understanding on the genetic program behind phytochrome developmental time dependent control of leaf 3 (L3) cell proliferation and expansion phases, to ultimately regulate organ growth. Briefly, Arabidopsis thaliana Col-0 plants were grown under a light : dark (LD) 12 h : 12 h photoperiod, at a 100 µmoles/m2/s fluence rate and 21 °C of constant temperature. Plants were then exposed to either daily End of Day (EoD) far-red (FR, 40µmoles/m2/s of FR light (730nm) for 10 minutes) from day 6 and harvested L3 primordia or blade tissue at days 13, 16 and 20, or EoD FR from day 18, sampling at day 20. Plant kept under white light (WL) conditions were used as controls.
2021-02-18 | E-MTAB-9445 | biostudies-arrayexpress