Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence. Two-condition experiment, wild type vs. pif quadruple mutant. Biological replicates: 3 wild type replicates, 3 mutant replicates.
Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence.
Project description:The total mRNA and polysomal RNA expression profiles of wild type (Col-0) and the quadruple spa mutant (spaQ) were analyzed under dark or in 4 hour light treated condition. The gene expression changed in spaQ mutant was analyzed and compared with Col-0.
Project description:Protein abundance and phosphoproteome profiling of wild-type (WT) as well as quadruple mutant plants deficient in G alpha, G beta, and two out of the three G gamma subunits, in Arabidopsis. WT plants are Col-0 and the quadruple mutant consists ofgpa1-4, agb1-2, agg1-1, and agg2-1 mutants.
Project description:Transcriptional profiling of 60h-old Arabidopsis whole seedlings comparing control Col-0 wild-type plants with pifQ mutant plants The expression profile of dark-grown pifQ mutant shows similar pattern of Rc-grown Col-0 wild-type Keywords: Genetic modification
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.
Project description:rs12-08_cyp715a1 - col-0 vs cyp715a1 - The microarray analysis is part of a project aimed at characterizing the function of the cytochrome P450 CYP715A1 in Arabidopsis thaliana. - Flower buds of Arabidopsis Col-0 (wild-type) and cyp715A1 mutant were harvested for a comparative analysis of their transcriptomes.
Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.
Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the small RNA sequencing. Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the small RNA sequencing.
Project description:We report the application of illumina high throughput RNA sequencing for rrc1-3 mutants in both light and dark conditions(three replicates under each condition) in Arabidopsis. By obtaining over 100 million reads (150bp paired_end) for each rRNA depleted lib, we compared the transcriptome profile between rrc1-3 mutant and Col-0 wild type light and dark conditions. We find that genome wide spliciing activities are general defective in rrc1-3 mutant comparing to Col-0 wild type, which indicates the importance of post-transcriptional processing on gene expression regulation. In addition, the sequencing data also indicates light signal probably regulates both splicing cascade and transcriptional cascade to control the downstream gene expression.
