READ ME File For 'Dataset supporting the University of Southampton Doctoral Thesis "Effects of active ingredients from Limonium Sinense (Girard) Kuntze extracts: a potential link with hypoxia-inducible factor (HIF) activation"'

Dataset DOI: 10.5258/SOTON/D2989

ReadMe Author: Hualong Zhao, University of Southampton ORCID ID: 0000-0002-5009-1444

This dataset supports the thesis entitled: Effects of active ingredients from Limonium Sinense (Girard) Kuntze extracts: a potential link with hypoxia-inducible factor (HIF) activation 
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2024

DESCRIPTION OF THE DATA
This study investigated the effects of bioactive ingredients from Limonium Sinense and elucidated their underlying mechanisms. The therapeutic effects of Limonium Sinense were predicted using a network pharmacology approach. The active ingredients of Limonium Sinense were collected from published literature, and the potential targets related to Limonium Sinense were obtained from public databases. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and DisGeNET enrichment analyses were performed to explore the underlying mechanisms. Molecular docking and Gene Expression Omnibus (GEO) datasets were employed to further evaluate the findings. Integrated analysis including bioinformatic analysis and in vitro experiments was employed to explore the effects of bioactive ingredients from Limonium Sinense, such as CellTiter-Glo® Luminescent cell viability assay was performed in 2D- and 3D-cultured cells, as well as flow cytometry, qRT-PCR, western blot, immunofluorescence microscopy and luciferase reporter analyses. RNA-seq coupled with bioinformatics was utilized to characterize the global transcriptomic changes and biological effects. HPLC was used to identify the components within Limonium Sinense. A structure-based virtual screening approach was conducted to identify potential inhibitors of prolyl hydroxylase domain protein 2 (PHD2) from Hydroxybenzoic acids and their derives.

This dataset contains: The dataset includes three zipped files: Part  I, Part II and Part III. Part I is the raw data for the published paper "Integrated analysis reveals effects of bioactive ingredients from Limonium Sinense (Girard) Kuntze on hypoxia-inducible factor (HIF) activation". Part II is the raw data for the published paper "Integrated network pharmacology and cellular assay reveal the biological mechanisms of Limonium sinense (Girard) Kuntze against Breast cancer". Part III is the raw data for the "Chapter 5 Identification of small molecules as potential inhibitors of PHD2 from Hydroxybenzoic acids and their derives using structure-based virtual screening" in the thesis. All the raw data is in excel format as well as powerpoint and images supporting the data.




Date of data collection: 01/03/2024

Information about geographic location of data collection: Southampton, United Kingdom / Yancheng city, China

Licence:
CC BY

Related projects/Funders:
Medical Research Council [grant no: MR/S025480/1]
Academy of Medical Sciences/the Wellcome Trust Springboard Award [grant no: SBF002/1038]

Related publication:
Hualong Zhao, Siyuan Wang, Philip T F Williamson, Rob M Ewing, Xinhui Tang, Jialian Wang, Yihua Wang. Integrated network pharmacology and cellular assay reveal the biological mechanisms of Limonium sinense (Girard) Kuntze against breast cancer. BMC Complement Med Ther, 2023, 23(1):408. doi: 10.1186/s12906-023-04233-z.

Hualong Zhao, Siyuan Wang, Yilu Zhou, Ayse Ertay, Philip T.F. Williamson, Rob M. Ewing, Xinhui Tang, Jialian Wang, Yihua Wang. Integrated analysis reveals effects of bioactive ingredients from Limonium Sinense (Girard) Kuntze on hypoxia-inducible factor (HIF) activation. Front Plant Sci, 2022. 13: p. 994036. doi: 10.3389/fpls.2022.994036.


Date that the file was created: March, 2024