Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for comparative coverage aspects with plant-RRBS methylome profiling by bioinformatics analyses. The inbred control line and a derived epiline LR2 of the 4th selfing were analysed using whole-genome bisulfite sequencing.
Project description:Purpose: this study provided a comprehensive sequence for a systemic view of the transcriptome between mango leaf and fruit, as well as fruit allergens, which will be useful for further genomic research studies and breeding of lower allergenic mango cultivars. Methods:Some allergens have previously been identified in mango (Mangifera indica Linn), including profilins, Bet v 1-like proteins and chitinase. In this paper, 66 potential allergen genes were identified and their relative expressions evaluated in mango fruit and leaf using Illumina RNA-Seq technology. Results:A total of 17.63Gb Clean Data was obtained.The number of %≥Q30 was above 94.58%.RNA-Seq generated 11,751,123 contigs that were assembled into 99,328 unigenes with 16,848 unigenes of >1000 bp. A total of 230,242 unigenes were annotated using public protein databases, with a cut-off E-value above 10−5, of which 27,295, 46,030, 24,227 and 14,023 unigenes were assigned to gene ontology terms, Nr, Swiss-Prot and clusters of orthologous groups, respectively. Allergens mainly belonged to pollen allergen, pathogenesis-related protein Bet v I family and NADPH-dependent FMN reductase.
Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for WGBS analysis. The inbred control line and derived epilines LR1, LR2 and LR3 of the 4th selfing were analysed using whole-genome bisulfite sequencing. Control and LR2 lines can be found in ArrayExpress E-MTAB-5002 submission, LR1 and LR3 are part of this submission
Project description:The contained data consist of Illumina NextSeq reads generated genomic DNA of Oryza sativa ssp. indica used for ChIP-seq analysis. The inbred control line and a derived epiline LR2 of the 5th selfing were analysed using chromatin immunoprecipitation sequencing.
Project description:Pot grown plants of Arabidopsis thaliana, Cardamine hirsuta, Cardamine pratensis, Rorippa palustris and Rorippa sylvestris where completely submerged under ambient light conditions. After 24 and 48 hours the shoots were harvested for expression analysis. Differential expression analysis, taking into account unsubmerged control plants revealed that the Rorippa genus had a pronounced down regulation of the cell cycle whereas the Cardamine had an attenuated response to submergence.
Project description:Purpose: The chloroplast DNA has not been primiarly analyzed in rice plants before. Hence, the objective of this study is to analyze and compare the differential methylation of chloroplast DNA in MR219 indica rice across different tissues and different developmental stages. Methods: We prepared a total of nine sodium bisulfite treated DNA libraries from three developing grain tissues, three leaf tissues at ripening stage and three leaf tissues at vegetative stage and sequenced them in Illumina Miseq platform. We performed quality trimming, alignment followed by methylation calling and differential methylation analysis using Trimmomatic v36, Bismark v16.3 and SeqMonk v40.0 on the sequencing data obtained. Statistical analysis was carried out in SeqMonk software and further validated in SPSS statistical software v22.2. Results: With an optimized data analysis workflow, we mapped around average of 26000 reads to chloroplast genome. Differential CpG and CHG methylation in SeqMonk v40.0 revealed that MR219 chloroplast DNA is differentially methylated in grain and leaf tissues and across vegetative stage and ripening stage in the leaf tissues. Chloroplast DNA from leaf at ripening stage was most methylated, followed by grain tissue and lastly leaf tissue from vegetative stage. Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated.
Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.