DaLitOffi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB79875 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13670008_1.fastq.gz | Fastqsanger.gz | |||
| ERR13670008_2.fastq.gz | Fastqsanger.gz | |||
| ERR13660051.fastq.gz | Fastqsanger.gz |
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Project description:Nasturtium officinale, genomic and transcriptomic data
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Project description:Dendrobium officinale is a common and expensive traditional Chinese medicine used as a medicinal agent and food that has immunoregulatory and anti-inflammatory effects. Methods to authenticate D. officinale are lacking. Although chemical profiles of D. officinale were published, transcriptomic profiling is lacking. Here, we collected D. officinale from two regions (Yunnan and Miandian) and the analogue D. compactum. The Yunnan samples had three different quality levels. All samples were subjected to genome-wide biological response fingerprinting (BioReF) in RAW264.7 cells using RNA sequencing.
2024-04-07 | GSE171632 | GEO
Project description:Mycorrhizal fungi colonize orchid seed and induce the germination. This so-called symbiotic germination is a critical developmental process in the lifecycle of all orchids. However, the molecular changes taking place during the orchid seed symbiotic germination still remains largely unknown. To better understand the molecular mechanism of orchid seed germination, we performed comparative transcriptomic and proteomic analysis on Chinese traditional medicinal orchid plants, Dendrobium officinale to explore protein expression change at the different developmental stages between asymbiotic and symbiotic germination and identify the key proteins regulated symbiotic germination of orchid seeds. iTRAQ analysis from 8 samples identified 2256 plant proteins, of which, 308 proteins were differentially expressed across three developmental stages within asymbiotic or symbiotic accession and 229 proteins are differentially expressed in the symbiotic germination compared to asymbiotic germination. 32 proteins are co-upregulated in both proteomic and transcriptomic level for symbiotic germination compared to asymbiotic germination. Our results revealed that symbiotic germination of D. officinale seeds probably shares the common signal pathway with asymbiotic germination during the early germination stage.
2017-05-12 | PXD006102 | Pride
Project description:In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 3 tissues of L. officinale. RNA sequencing and de novo transcriptome assembly of L. officinale resulted in a total of 77,047 unigenes with N50 value as 1524 bps. KEGG pathway and GO enrichment analysis using highly expressed unigenes across three tissues showed active secondary metabolic processes specifically enriched to the root of L. officinale. Expression of identified candidate unigenes for specialized metabolites biosynthesis were consistent with previous reports on accumulation of metabolites across different tissues of L. officinale.
2018-07-01 | GSE111375 | GEO
Project description:Background: Dendrobium officinale, an endangered Chinese herb, has extensive therapeutic effects and contains bioactive ingredients including a large number of polysaccharides and alkaloids, and minimal flavonoids. Firstly, this study attempts to obtain the protocorm-like bodies of this plant through tissue culture to produce the main secondary metabolites whose distribution in each organelle and protocorm like bodies is analyzed. Then, analysis of the correlation between comparative transcriptome sequence and the metabolite content in different organs enables the discovery of putative genes encoding enzymes involved in the biosynthesis of polysaccharides and alkaloids, and flavonoids. Results: The optimum condition for protocorm-like bodies (PLBs) induction and propagation of D. officinale is established. For protocorm induction, we use the seed as the explant, and the optimum medium formula for PLBs propagation is 1/2 MS + α-NAA 0.5 mg·L-1 +6-BA 1.0 mg·L-1 + 2, 4-D 1.5-2.0 mg·L-1 + potato juice 100 g·L-1. The distribution of polysaccharides, alkaloids and flavonoids in D. officinale organs was clarified. Stems, PLBs and leaves have the highest content of polysaccharides, alkaloids and flavonoids, respectively. PLBs replace organs to produce alkaloids in D. officinale, and naringenin was only produced in stem. Hot water extraction (HWE) method was found outperforming the ultrasound-assisted extraction (UAE) method for polysaccharides from D. officinale. A comparative transcriptome analysis of the protocorm-like bodies and leaves of D. officinale showed genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids biosynthetic pathway were differentially expressed. Putative genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids synthetic pathway were identified. Notably, genes encoding enzymes of strictosidine beta-glucosidase, geissoschizine synthase and vinorine synthase in alkaloids biosynthesis of D. officinale are first reported. Conclusions: Our works, especially the identification of candidate genes encoding enzymes involved in metabolites biosynthesis will help to explore and protect the endangered genetic resources and will also facilitate further analysis of the molecular mechanism of secondary metabolites’ biosynthesis in D. officinale.
2021-04-24 | GSE155403 | GEO
Project description:Dendrobium officinale is a traditional medicinal herb with a mount of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. A total of 4857 DEGs, including 2943 up- and 1932 down-regulated genes, were identified between the control and MeJA-treated groups. Several shikimate and methylerythritol 4-phosphate pathway genes and a number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the alkaloid metabolism in D. officinale.
2019-01-07 | GSE124762 | GEO