Project description:We used Affymetrix Arabidopsis ATH1 GeneChip to profile RNAs active in wild type columbia (glabrous) and CaMV::DME pollen and stamens. Keywords: genetic modification
Project description:Investigation of the ecotype difference between Columbia-0 (Col) and Wassilewskija-0 (WS) on whole gene expression level, of PME17 mutation effect (compared to background WS) and of the aphid infestation effect on Col, WS and pme17 (infested plants compared to non-infested plants).
Project description:We used Affymetrix Arabidopsis ATH1 GeneChip to profile RNAs active in wild type columbia (glabrous) and CaMV::DME pollen and stamens. Experiment Overall Design: DME is not active in wild type pollen and stamen. DME was induced in pollen and stamen by a cauliflower mosaic virus promoter (CaMV). RNA profiles from wild type and CaMV::DME pollen and stamens were compared using Affymetrix ATH1 GeneChip.
Project description:To comprehensively investigate the effects of glutathione on the gene expression, the microarray analysis was performed in the glutathione-fed wild-type Arabidopsis thaliana. Wild-type Arabidopsis (ecotype Columbia-0) were fed with 1 mM oxidized glutathione (GSSG) and 2 mM reduced glutathione (GSH) for comparison at equal nitrogen equivalents. To examine the effects of glutathione other than nitrogen at equal nitrogen equivalents, plants were fed with 3 mM NH4NO3. Plants grown by water were used as a control.
Project description:Pollen grains of Arabidopsis thaliana contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein coding genes expressed in pollen, including 289 assayed only by non-specific probe sets. Additional exons and previously unannotated 5’ and 3’ UTRs for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 confirmed by PCR. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of on-going annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.
