Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large scale cell-based transcriptome data treated with Jakyakgamcho-tang in HepG2 cell

ABSTRACT: Jakyakgamcho-tang (JGT) is the simplest form of herbal medicine composed of Paeoniae Radix (PR) and Glycyrrhizae Radix at Rhizoma (GR), and has been used to treat muscle-related diseases and inflammation. However, the pharmacological effects of JGT may vary depending on the ratio of the constituent herbs and the main preparation conditions of the extraction method. Nevertheless, no gene expression dataset systematically reflecting these various variables has existed to date. In this study, a total of 498 transcriptome profiles were constructed with three concentrations and three replicates of RNA-seq data. It is structured to enable multidimensional analysis of the effects of various preparation conditions on gene expression by combining the ratio of PR:GR (2:1, 1:1, 1:2), solvent (water, 70% ethanol), and extraction method (combined decoction vs. separate decoction) of JGT, targeting three cell lines (HepG2, C2C12, and PC12). All raw and preprocessed data are deposited available through GEO, and standardized metadata and ingredient data are also provided. This dataset provides a foundation for exploring how traditional herbal medicine formulations affect cellular transcriptomic responses and can serve as a baseline for scientific optimization of herbal medicines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE299063 | GEO | 2025/10/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Jakyak-gamcho-tang ameliorates dexamethasone-induced muscle atrophy and muscle dysfunction [C2C12]

Project description:Jakyak-gamcho-tang (JGT) is a herbal medicine that has been traditionally prescrived for pain control including muscular pain. This transcriptome analysis aims to investigate the changes in global gene expression profile in differentiated murine C2C12 myotube cells treated with JGT extract.

2023-03-21 | GSE227494 | GEO

The analysis of gene transcription and the effect of drug resistance of Radix Paeoniae Rubra Decoction on Staphylococcus aureus

Project description:To study the effect of Radix Paeoniae Rubra decoction on tolerance of Staphylococcus aureus.The effect of Radix Paeoniae Rubra on the resistance of Staphylococcus aureus to oxacillin sodium was studied by millipore dilution method in this experiment.At the same time ,conducted on transcriptome analysis of Staphylococcus aureus related genes in Radix Paeoniae Rubra.And to detect the expression level of related genes of Staphylococcus aureus under the action of Radix Paeoniae Rubra by PCR technology.The tolerance of Staphylococcus aureus was decreased obviously when the concentration of Radix Paeoniae Rubra decoction was above 1mg/ml.The effect of Radix Paeoniae Rubra decoction on the expression of tolerance genes femB,pvL and gluM when the concentration of Radix Paeoniae Rubra decoction was above 4mg/ml.When rhe concentration of Radix Paeoniae Rubra is more than 1mg/ml,it can effectively reduce the resistance of Staphylococcus aureus to oxacillin sodium.The reason may be due to the effect of Radix Paeoniae Rubra on the resistance gene of Staphylococcus aureus.

2021-01-30 | GSE165791 | GEO

Jakyak-gamcho-tang ameliorates dexamethasone (DEX)-induced muscle atrophy and muscle dysfunction [Gastrocnemius and Soleus]

Project description:Jakyak-gamcho-tang (JGT) is a herbal medicine that has been traditionally prescrived for pain control including muscular pain. Muscle atrophy is a disease that is characterized with a gradual muscle loss. Muscle atrophy is clearly observed in experimental animals that receive a repeated high-dose of an artificial glucocorticoid, dexamethasone (DEX). This transcriptome analysis aims to investigate the changes in global gene expression profiles in gastrocnemius (GA) and soleus (SO) muscle tissues from mice with DEX-induced muscle atrophy in the presence or absence of JGT co-treatment.

2023-03-21 | GSE227495 | GEO

Transcriptomic study of the mechanism by Kai Yu Zhong Yu (KYZY) recipe to improve oocyte quality in the stressed mouse model

Project description:Female ICR mice were treated with stress or stress plus herbal medicine (KYZY decoction) in chronic unpredictable mild stress (CUMS) model. Fifteen isolated oocytes from each mouse were used for RNA-seq analysis. We used DESeq2 to identify differentially expressed genes (DEGs) between groups. DAVID and GO resources were used to perform gene enrichment analysis on the DEGs.

2022-02-14 | GSE152754 | GEO

In-depth analysis of molecular network based on LC-MS/MS in complex systems

Project description:Ginseng Radix et Rhizoma (GR), Bufonis Venenum (BV), Epimedii Folium (EF), Aconiti Lateralis Radix Praeparata (AL) and Salviae Miltiorrhizae Radix et Rhizoma (SM)

2023-11-27 | MSV000093516 | MassIVE

Transcription profiling of human U937 lymphoma cells treated with paeony root (Paeoniae radix) (time series)

Project description:Paeoniflorin (PF) isolated from paeony root (Paeoniae radix) has been used as an herbal medicine in East Asis for its anti-allergic, anti-inflammatory, and immunoregulatory effects. PF is known to be a chemical heat shock protein (HSP) inducer. The effects on the gene expression in human lymphoma U937 cells treated with PF were investigated using by an Affymetrix GeneChip system. PF treatment induced Hsp70 expression in U937 cells in a dose- and time-dependent manner as shown in Western blot analysis. When the cells were treated with PF (160 Î¼g/ml; 30 min), 41 up-regulated and 23 down-regulated genes were identified. Experiment Overall Design: U937 cells, a human lymphoma cell line, were treated with paeoniflorin (0.16 mg/ml; 30 min) and followed by incubation for 0, 3, and 6 h at 37Â°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with Human Expression Array U133A which was spotted with 22,283 probe sets. Sample preparation for array hybridization was carried out as described in the manufactureâs instructions.

2008-06-16 | E-GEOD-8228 | biostudies-arrayexpress

Optimizing Personalized Therapy for Rheumatoid Arthritis Using a Novel Drug Combination of Bioactive Chemical Constituents Derived from a Classic Chinese Herbal Formula

Project description:Personalized therapy of rheumatoid arthritis (RA) based on traditional Chinese medicine cold and hot syndromes is selection of the best treatment for an individual patient. Wutou Decoction (WTD) is one of the classic Chinese herbal formulae which achieve favorable therapeutic response in treating RA-cold syndrome. Microarray analysis based on the adjuvant induced arthritis model combined with characteristics of RA and cold/hot syndromes was performed to screen RA-cold and RA-hot-syndrome-related genes, as well as WTD effect genes.

2018-06-13 | GSE115662 | GEO

Translation deficits drive C9orf72 associated poly-GR/PR toxicity

Project description:Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) patients with the C9orf72 mutation show predominantly cytoplasmic aggregates of poly-GR and poly-PR proteins that are acutely toxic in various model systems. To identify the molecular mediators of neurotoxicity of poly-GR/PR, we analyzed their interactomes in primary neurons. GFP-(GR)149 and (PR)175-GFP preferentially interacted with RNA-binding proteins, including stress granule-associated and nucleolar proteins, as well as ribosomes. Overexpression of the poly-GR/PR interactors Staufen 1/2 (STAU1/2) and YBX1 led to cytoplasmic aggregation of poly-GR/PR into large stress granule-like inclusions, while the poly-GR/PR interactor nucleophosmin (NPM1) recruited poly-GR into the nucleolus. In addition, poly-PR expression reduced ribosome levels and translation, which is consistent with the widespread reduction of synaptic proteins detected by proteomics. Surprisingly, only GFP-(GR)53, but not GFP-(GR)149, localized to the nucleolus and reduced ribosome levels and translation in neurons, suggesting impaired ribosome biogenesis is driving the acute toxicity commonly observed in vitro. In C9orf72 patient brains, we detected co-aggregation of poly-GR/PR inclusions with ribosomes, but not stress granules. Partial sequestration of ribosomes may chronically impair protein synthesis and contribute to C9orf72 ALS/FTD pathogenesis.

2018-06-27 | PXD008691 | Pride

Chinese Herbal Formula (GCNY)-Medicated Serum Alleviates Peroxidation Induced by H2O2 in Human Microglial Cells

Project description:Transitional Chinese herbal medicine has a long history of applications for anti-aging and longevity purposes, and in our patent formula Gancao Nurish-Yin (GCNY) decoction, all of the ingredients show antioxidant properties. However, in real clinical practice, extractions of herbs are rarely applied alone but are prescribed as integrated formula. In order to investigate whether GCNY possess anti-oxidation potential, we applied GCNY as a formula to treat rats in order to acquire medicated serum, which was then added on H2O2 (200 μM)-modeled human microglial cell line HMC-3 in comparison with its controls.

2022-09-06 | GSE210945 | GEO

Effects of maoto (ma-huang-tang) on transcriptome signature in influenza virus infection

Project description:We evaluated the effects of maoto, a traditional kampo medicine, as a herbal multi-compound medicine on host transcriptome responses in a mouse model of influenza infection. On the fifth day of oral administration to mice intranasally infected with influenza virus (A/PR/8/34 (H1N1), maoto significantly improved survival rate, decreased viral titer, and ameliorated the infection-induced phenotype as compared with control mice. Analysis of the lung and plasma transcriptome profile showed that maoto significantly up-regulated the expression of macrophage- and T-cell-related genes. Collectively, these results suggest that maoto regulates the host’s inflammatory response.

2021-10-21 | GSE158270 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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