Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo transcriptome assembly based RNA-Seq and dynamic expression of key enzyme genes in baicalin biosynthetic pathway of Scutellaria baicalensis Georgi

ABSTRACT: Scutellaria baicalensis Georgi, a perennial herb, is an important medicinal plant that possesses broad pharmacological actions and contains flavonoids with good bioactivities such as anti-inflammation, anti-bacteria and anti-tumor. However, little is known on the molecular processes responsible for the medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of S. baicalensis were first generated and used for transcriptome analysis.

ORGANISM(S): Scutellaria baicalensis

PROVIDER: GSE132061 | GEO | 2022/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic analysis and dynamic expression of genes revealed flavonoid synthesis in Scutellaria viscidula

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

MicroRNA expression profiling of hepatocellular carcinoma cell line BEL-7402 treated with baicalein

Project description:Baicalein, a purified flavonoid compound with defined chemical structure extracted from the dry roots of Scutellaria radix that is a broadly used herb in China, has been proved to possess significant anti-hepatoma activity by inhibiting cell proliferation, invasion, metastasis and inducing apoptosis, autophagy via several cancer-related signaling molecules. In recent years, emerging studies have demonstrated that Chinese medicinal herbs can exert their anti-tumor effects through targeting miRNAs，such as curcumin, camptothecin, resveratrol. However, there is still no related report about the effects of baicalein on miRNA expression profile when it exerts its inhibition on hepatoma tumor growth. To investigate whether the antitumor effect of baicalein is related to its modulation of miRNA expression in hepatocellular carcinoma (HCC), we profiled the miRNA expression in HCC cell line Bel-7402 treated with baicalein (0, 40, 80μM) for 24 hours using miRNA microarray and detected the changes by comparing the miRNA expression profile of HCC cell line Bel-7402 treated with baicalein (40 and 80 μM) and its DMSO control (0 μM). These findings suggest that modulation of miRNA expression may be an important mechanism underlying the anti-hepatoma effects of baicalein and lay the groundwork for further investigations.

2017-08-15 | GSE85511 | GEO

Scutellaria baicalensis cultivar:Georgi

Project description:Scutellaria baicalensis cultivar:Georgi Raw sequence reads

| PRJNA309619 | ENA

Discovery and mechanistic studies of cytotoxic cyclotides from the medicinal herb Hybanthus enneaspermus (Linn) F. Muell

Project description:Cyclotides are a family of plant-derived peptides characterized by a ~30 amino acid cyclic backbone and a cystine knot motif. Cyclotides have diverse bioactivities, and in particular their cytotoxicity has attracted significant attention for its potential anti-cancer applications. Hybanthus enneaspermus is a medicinal herb widely used in India as a natural libido enhancer, and a previous study indicated that it may contain cyclotides. In the current study, 11 novel cyclotides and one known cyclotide (cycloviolacin O2) were identified and isolated from H. enneaspermus. Their sequences were determined using tandem MS, and NMR analysis of six of these cyclotides indicates their three-dimensional structures are similar to those of other known cyclotides. The most abundant cyclotide in this plant, hyen D, has comparable cytotoxicity against cancer cells to cycloviolacin O2, the most cytotoxic cyclotide discovered so far. Herein we provide a mechanistic insight into the mode-of-action of the novel cyclotides’ cytotoxicity. Hyen D, E, L, M, and cycloviolacin O2 preferentially interacted with model lipid membranes containing phospholipids with phosphatidylethanolamine-headgroups, as measured by surface plasmon resonance. Cyclotide-membrane interactions correlated with cytotoxicity, suggesting that membrane binding underpins cytotoxicity. Overall, this study helps broaden knowledge on the indigenous Indian herb H. enneaspermus, and reports the discovery of novel cyclotides with potent anti-cancer activity.

2020-05-13 | PXD017924 | Pride

De novo transcriptome assembly based RNA-Seq and dynamic expression of key enzyme genes in baicalin biosynthetic pathway of Scutellaria baicalensis Georgi

Project description:De novo transcriptome assembly based RNA-Seq and dynamic expression of key enzyme genes in baicalin biosynthetic pathway of Scutellaria baicalensis Georgi

| PRJNA545800 | ENA

RNA-seq of various organs of Potentilla indica and Melastoma dodencadrum Lour.

Project description:Potentilla indica and Melastoma dodecandrum lour are medicinal herbs used in traditional Chinese medicine. We sampled the plants from Nanyang Technological University's herb garden for transcriptomics analysis.

2023-03-21 | E-MTAB-12682 | biostudies-arrayexpress

Chlorophytum borivilianum

Project description:Annual herb of medicinal value

| PRJNA32621 | ENA

Transcriptome analysis of basal and luminal cells treatment with baicalin

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.

2021-02-05 | GSE166157 | GEO

Smilax glabra flavonoids treatment of 3T3-L1 adipocytes

Project description:Smilax glabra Roxb, a traditional Chinese herb, has been widely used for folk medicine. Previous studies have found that it has various pharmacological activities, such as cytotoxic, anti-inflammation, anti-oxidant, hepatoprotective, and cardiovascular system protective activities. However, its roles in adipogenesis are poorly understood. We hypothesized that Smilax glabra Roxb and its main component may play important roles in regulating adipocyte diffrentiation and function. To test this hypothesis, we performed RNA-Seq on 3T3-L1 adipocytes treated with and without pure total flavonoids from Smilax glabra Roxb.

2022-01-11 | GSE124950 | GEO

Transcriptomic responses to cold stress in Dendrobium huoshanense C.Z. Tang et S.J. Cheng

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.

2022-11-10 | GSE217439 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data