Project description:To elucidate the sucrose signaling and the defense marker genes under sucrose treatment. This gene is intended for functional analysis. In addition, the underlying molecular mechanisms of this defense marker were studied. After that, investigate the underlying molecular mechanisms from sucrose treatment to pathogen defense pathway were studied.
Project description:We created a double loss-of-function/knockout mutant targeting two rice genes simultaneously. The selected genes are as follows: OsCNGC4(LOC_Os03g44440) and OsCNGC5(LOC_Os12g28260). These two CNGCs are strongly transcriptional expressed in the rice mature anthers (stages 13-14). The mutant of these OsCNGC4/5 displayed a low seed-setting rate. This data refers to the transcriptome of mature anthers from the double mutant of OsCNGC4 and OsCNGC5. We sampled mature anther for the analysis.
Project description:A RPE cell model mimicking a matured RPE was subjected to an acute inflammatory stress with and without Zn supplementation and the effects of such exposure were evaluated by studying alterations at the transcriptome level. The experiment performed aim to improve the understanding of the metabolic processes involving Zn and their relevance in the physiology and pathophysiology of neurodegenerative diseases resembling AMD disease.
Project description:Rice anthers at anthesis stage from the wild type and osrac6-1 mutant anther (Dongjin cultivar) We collected the sample from our field and immediately froze the samples with liquid nitrogen.
Project description:Pollen tube growth is essential for successful fertilization and stable crop yields. We constructed loss-of-function/knock-out mutants that simultaneously target two rice genes using the CRISPR/Cas9 mutagenesis system. The selected OsRALF17 and OsRALF19 genes are strongly expressed in rice bicellular/tricellular pollen and have essential functions in the pollen tube growth. For the corresponding transcriptomic analysis, we sampled mature pollen anthers from a control group and an OsRALF17/19 knock-out mutant.
Project description:We created a triple loss-of-function/knockout mutant targeting three rice genes simultaneously. The three selected genes are as follows: OsADF1 (LOC_Os02g44470), OsADF6 (LOC_Os04g46910), and OsADF9 (LOC_Os07g30090). These three ADFs are strongly transcriptional expressed in the rice mature anthers (stages 13) and bi-/tricelluler pollen. The triple mutant of these OsADFs does not produce self-fertilizing seeds due to the short length of the pollen tube (male-sterile). This data is about mature anther transcriptome data about the triple mutant of OsADFs (ADFmT). We sampled mature anther for the analysis.
Project description:Seven temperature sensitive Saccharomyces cerevisiae BY4741 mutants (rsc3-1, abf1-101, reb1-212, rap1-1, mcm1, tbf1 and cep3-1) were grown at restrictive temperatures until a difference in OD600 was observed relative to a wild-type control. Nucleosomal DNA, whole genomic DNA and total RNA were isolated and hybridized onto yeast whole-genome tiling arrays.<br>
Project description:microRNA transcriptome data from wild type and Gata6-deficient tissue resident peritoneal macrophages. Tissue resident macrophages are notoriously heterogeneous, exhibiting discrete phenotypes as a consequence of tissue- and micro-anatomical niche-specific functions, but the molecular basis for this is not understood. Gata6 itself has been shown to be a target of multiple miR. However, microRNA transcriptome and its dependence on tissue-specific macrophage programming, such as effected by GATA6, has not been explored. We used microRNA sequencing to determine the patterns of microRNA expression in peritoneal resident macrophages at homeostasis in the absence of GATA-6 against wild type.
Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.