Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19581682_1.fastq.gz | Fastqsanger.gz | |||
| SRR19581682_2.fastq.gz | Fastqsanger.gz | |||
| SRR19581683_1.fastq.gz | Fastqsanger.gz | |||
| SRR19581683_2.fastq.gz | Fastqsanger.gz | |||
| SRR19581684_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
2022-02-23 | PXD008958 | Pride
Project description:The tea plant (Camellia sinensis (L.) O. Kuntze) is often commercially used as a source of non-alcoholic beverages and is an economically important woody crop (Chen et al., 2007). As living standards have improved, the requirement for high-quality life has increased in modern society. ‘Anji Baicha’ (alias ‘Baiye 1’ or ‘White Leaf 1’) is an excellent tea cultivar with albino phenotype and it is popular in producing high-quality green tea. The traits of ‘Anji Baicha’ are as follows. Young ‘Anji Baicha’ shoots are yellow-green when the early spring temperature is below 20°C. As the leaves fully expand, the leaves become white. The leaves gradually return to green when the environmental temperature increases (Cheng et al., 1999; Li et al., 2002, 2011). Previous reports have suggested a positive correlation between amino acid concentration and albinism as well as a negative correlation between tea polyphenols and albinism (Li et al., 1996; Du et al., 2006; Xiong et al., 2013). Therefore, the quality of ‘Anji Baicha’ is much higher when new shoots become albino due to their rich amino acid content and modest tea polyphenol content. Plants adjust their metabolism in response to environmental stimuli to eventually bring about changes in protein activities and levels, and this adaptive process includes posttranslational protein modifications (PTMs) (Prabakaran et al., 2012). PTMs have been reported to regulate various processes, including DNA interaction, protein-protein interactions, enzyme activation and protein stability. Among the hundreds of different PTMs, lysine acetylation is an abundant, reversible and highly regulated PTM (Zhang et al., 2009; Wu et al., 2011).
2018-01-15 | PXD008134 | Pride
Project description:The green tea made from the etiolation shoots and leaves have fresh taste and strong aroma. ‘Zhonghuang 2 (ZH2) is a natural etiolation mutant and its shoots are etiolation in spring and turn green in summer. Two conditions including the relative high temperature (LT, 26 / 22oC) and the relative low temperature (LT, 18 / 14oC) were to find out the etiolated reason of ZH2. We confirmed ZH2 was a low-temperature sensitive tea plant cultivar, and the reason of shoots etiolation at LT was the reduction of stacked grana, which could cause the lack of photoreaction. We identified 1279 differentially expressed genes (DEGs), most of them were related to cytochrome synthesis and chloroplast development and function by RNA-seq. Through the whole-genome bisulfite sequencing (WGBS) assay, we found that the dynamic of DNA methylation level in three contexts (CG, CHG and CHH) was all decreased at LT, and the change was most obvious in the CHH context. According the result of cross analysis, 56 genes were identified with significant changes in both expression and DNA methylation levels. A large number of them were related to chloroplast development and chlorophyll synthesis. This study demonstrated that the DNA methylation was involved in the low-temperature regulated etiolation process of young shoots in ZH2. Change of the DNA methylation level was associated with the gene expression level, thus affecting the structure and function of chlorophyll and chloroplast, even reduced photosynthesis, which might have a phenotypic impact on the color of shoots and leaves. And it laid the foundation for studying the etiolation process from an epigenetic perspective.
2023-10-19 | GSE234849 | GEO
Project description:Root-synthesized secondary metabolites are critical quality-conferring compounds of foods, plant-derived medicines, and beverages. However, information at a single-cell level on root-specific secondary metabolism remains largely unexplored. L-theanine, an important quality component of tea, is primarily synthesized in roots, from which it is then transported to new tea shoots. In this study, we present a single-cell RNA sequencing (scRNA-seq)-derived map for the tea plant root, which enabled cell-type-specific analysis of glutamate and ethylamine (two precursors of theanine biosynthesis) metabolism, and theanine biosynthesis, storage, and transport. Our findings support a model in which the theanine biosynthesis pathway occurs via multicellular compartmentation and does not require high co-expression levels of transcription factors and their target genes within the same cell cluster. This study provides novel insights into theanine metabolism and regulation, at the single-cell level, and offers an example for studying root-specific secondary metabolism in other plant systems.
2024-10-07 | GSE267845 | GEO
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant. In the study presented here, two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were kept at 4°C for 4,12, 24 h, respectively, and 28°C for as control. These samples were used to acquire expression profiles of a total of 3,511 unique genes, leading to the successful construction of supervised
2015-05-14 | E-GEOD-53632 | biostudies-arrayexpress
Project description:For developing the more SNPs and new high-density genetic linkage map of tea plant, two parents and their 326 progenies and 147 registered tea cultivars was sequencing by newly developed Affymetrix Axiom genotyping technology
2022-03-09 | GSE182082 | GEO
Project description:Next generation sequencing (NGS) was performed to identify genes changed in tea plant upon Colletotrichum camelliae infection. The goal of the work is to find interesting genes involved in tea plant in response to fungi infection. The object is to reveal the molecular mechanism of tea plant defense.
2024-07-18 | GSE208559 | GEO
Project description:Next-generation sequencing (NGS) was performed to identify genes changed in tea plant cultivar Zhongcha 108 upon Colletotrichum camelliae infection. The goal of the work is to find interesting genes involved in tea plant in response to fungi infection. The object is to reveal the molecular mechanism of tea plant defense.
2024-01-23 | GSE226846 | GEO
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.
2015-05-14 | GSE53632 | GEO
Project description:BACKGROUND: Evaluation of the airway transcriptome may reveal patterns of gene expression that are associated with clinical phenotypes of asthma. To define transcriptomic endotypes of asthma (TEA) we analyzed gene expression in induced sputum that correlate with phenotypes of disease. METHODS: Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays. Unsupervised clustering analysis of genes in pathways selected from the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified TEA clusters. Clinical characteristics were compared and logistic regression analysis of matched blood samples defined an expression profile to determine the TEA cluster assignment in a cohort of children with asthma for validation. RESULTS: Three TEA clusters were identified. TEA cluster 1 had the most subjects with a history of intubation (P = 0.05), a lower pre-bronchodilator FEV1 (P = 0.006), a higher bronchodilator response (P = 0.03), and higher exhaled nitric oxide levels (P = 0.04), compared to the other TEA clusters. TEA cluster 2, the smallest cluster had the most subjects that were hospitalized for asthma (P = 0.04). Subjects in TEA cluster 3, the largest cluster, had normal lung function, low exhaled nitric oxide levels, and lower inhaled steroid requirements. Evaluation of TEA clusters in children confirmed that TEA clusters 1 and 2 are associated with a history of intubation (P = 5.58 x 10-06) and hospitalization (P = 0.01), respectively. CONCLUSIONS: Patterns of gene expression in the sputum and blood reveal TEA clusters that are associated with severe asthma phenotypes in children and adults. Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays. Unsupervised clustering analysis of genes in pathways selected from the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified TEA clusters. Clinical characteristics were compared and logistic regression analysis of matched blood samples defined an expression profile to determine the TEA cluster assignment in a cohort of children with asthma for validation.
2014-04-07 | E-GEOD-56396 | biostudies-arrayexpress