Ontology highlight
ABSTRACT:
PROVIDER: PRJNA906931 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22461387_1.fastq.gz | Fastqsanger.gz | |||
| SRR22461387_2.fastq.gz | Fastqsanger.gz | |||
| SRR22461388_1.fastq.gz | Fastqsanger.gz | |||
| SRR22461388_2.fastq.gz | Fastqsanger.gz | |||
| SRR22461389_1.fastq.gz | Fastqsanger.gz |
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Project description:Baicalin is the main flavonoid component extracted from Scutellaria root. It has multiple potent biological activities, including estrogen-like activity. In our study, we investigated the function of baicalin on mammary stem cell proliferation and mammary development. Our results demonstrated that baicalin significantly accelerates mammary gland development at puberty and during pregnancy; In vitro, baicalin significantly promotes colony formation ability of mammary basal epithelial cells in a three-dimensional (3D) culture system; In vivo, baicalin improved mammary regeneration efficiency in mouse xenograft model. But the mechanism was unknown. Therefore, transcriptome analysis of basal and luminal cells treatment with baicalin was performed.
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Project description:Burkholderia cenocepacia J2315 biofilms were described to have an increased susceptibility towards tobramycin when baicalin hydrate was added to the treatment. The goal of this transcriptomic analysis is to elucidate the effect of baicalin hydrate on gene expression levels when added to tobramycin treatment. Therefore, biofilms were grown for 24 hours and treated for another 24 hours with either tobramycin (TOB) (1024ug/ml), baicalin hydrate (BH) (250uM) or a combination of both. Also, an untreated control (physiological saline) was included. This experiment was repeated twice, so three biological replicates per treatment were included for RNAsequencing.
2017-12-04 | E-MTAB-6099 | biostudies-arrayexpress
Project description:Scutellaria viscidula Bunge (Labiatae), a perennial herb, is an important medicinal plant that possesses broad pharmacological actions. S. viscidula contains flavonoids with good bioactivities (e.g. baicalin, wogonoside, baicalein and wogonin) mainly in its dry root, which is used as alternative to Scutellaria baicalensis in the north of China. Furthermore, S. viscidula also has flavones with interesting diverged structures such as panicolin, viscidulin I, viscidulin II and viscidulin III. Tracing the dynamic process of gene expression will help reveal the mechanism of flavonoid synthesis in S. viscidula, as well as the 4'-deoxyflavone biosynthesis in S. baicalensis. One way is to generate and analyze the expressed sequence tags (ESTs). However, little is known on the transcriptome information of S. viscidula, particularly the key genes involved in flavonoid biosynthesis. In this study, we conducted de novo transcriptome analysis of S. viscidula and obtained 42,310,834 reads and 40,052 unigenes, respectively. We revealed 177 genes relating to flavonoid biosynthesis, where 23 key enzyme encoding genes including CHS, CHI, F3H, PAL and 4CL were annotated. Furthermore, we investigated the dynamic expression of CHS, CHI, F3H, MYB2, and bHLH of stem, root and leaf of S. viscidula in May, July and September. Our results showed that these key genes had important regulatory function and exhibited positive correlation with total flavonoid content in different growth stages of S. viscidula. Collectively, this study provides high-quality transcriptome data of S. viscidula, and further gives significant information for understanding the molecular mechanism of gene expression and active ingredients in Scutellaria plants.
2020-12-27 | GSE108555 | GEO
Project description:Hickory (Carya cathayensis) is a woody plant with high nutritional and economic value, and is widely cultivated in China. It is different from herbaceous plants and undergoes a long vegetative stage before reaching floral transition. Hickory can be cultivated on a large scale using grafting. To reveal the response mechanisms to grafting, we employed a proteomics-based approach to identify differentially expressed proteins during the hickory grafting process. In our study, 3723 proteins were identified and 2518 proteins were quantified. A total of 710 differentially quantified proteins (DQPs) were identified and these were involved in various molecular functional and biological processes. Among these DQPs, 341 were up-regulated and 369 were down-regulated at 7 days after grafting compared to the control. The protein interaction networks of the DQPs indicated that there were two enriched interaction clusters. These were „ribosome‟ and „starch and sucrose metabolism‟. Four auxin-related proteins were down-regulated, which was in agreement with the transcription levels of their encoding genes. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the „Flavonoid biosynthesis‟ pathway was significantly up-regulated. Further experiments verified a significant increase in the total flavonoid contents in scions, which suggested that graft union formation may activate flavonoid biosynthesis to increase the contents of a series of downstream secondary metabolites. This comprehensive analysis provides fundamental information on the candidate proteins and the secondary metabolism pathways involved in the grafting process for hickory.
2018-10-26 | PXD006025 | Pride
Project description:Chayote (Sechium edule) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, a transcriptome analysis and metabolite profiling of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, we treated chayote fruits during storage with phenylalanine, and the results show exogenous phenylalanine applications might promote the flavonoid synthesis. Phenylalanine is a effective additive to maintain or improve the total content flavonoids in chayote fruit during storage, can apply the phenylalanine in the postharvest storage of chayote. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.
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Project description:Flowers at the full bloom stage were dipped into water (blank), 50 mg∙L-1 GA3 (gibberellic acid) or 3 mg∙L-1 CPPU. This was followed by a second application two weeks later onto young berries. Using integrated transcriptomic and proteomic analysis, differentially expressed transcripts and proteins associated with growth regulator treatment were identified including those for flavonoid biosynthesis that contribute to the changes in sensory astringency levels.
2024-01-17 | PXD042532 | Pride
Project description:Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a perennial epiphytic herb of family Orchidaceae, which main metabolites are polysaccharides, flavonoids, etc. Low temperature is the main environmental factor that limits the growth and development of plants, and even threatens the survival of plants. However, Changes that occur at the molecular level in response to low temperatures are poorly understood in D. huoshanense. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two time points of 0 d (control group) and 7 d (cold stress group). A total of 37.63 Gb transcriptomic data were generated using the MGI 2000 platform. These reads were assembled into 170,754 transcripts, and 23,724 differentially expressed genes (DEGs) were obtained. Pathway analysis indicated that “flavonoid biosynthesis”, “anthocyanin biosynthesis”, “flavone and flavonol biosynthesis”, and “plant hormone signal transduction” might play a vital role in D. huoshanense responses to cold stress. Several important pathways genes such as genes encoding polysaccharides, flavonoid, and plant hormone-signaling transduction kinase were identified under cold stress. In addition, the contents of mannose and total flavonoids increased under cold stress. Twelve DEGs in polysaccharides, flavonoid, and hormone pathways were selected from transcriptome analysis for quantitative real-time PCR (qRT-PCR) validation. Our results provide a transcriptome database and candidate genes for further study of D. huoshanense cold stress.
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Project description:Polyporus brumalis CIRM-BRFM 1820
| PRJNA265768 | ENA