RNA chip expression profiling analysis of HGC-27 cells after oxymatrine intervention, Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188) chip

In this study, we intervened HGC-27 cells with oxidized sophoridine alkaloid (OMT) at a concentration of 2.64 mg/mL for a duration of 48 hours. Subsequently, we conducted comprehensive chip expression profiling analysis on these intervened HGC-27 cells as well as normal HGC-27 cells, encompassing mRNA, lncRNA, and circRNA. We employed the Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188) chip for the expression profiling. To ensure analysis reliability, we quantified the total RNA of samples initially and then assessed the integrity of RNA using Agilent Bioanalyzer 2100 (Agilent Technologies). Following RNA quality inspection, we followed a standardized procedure to label the samples and hybridize them with the chips, followed by elution. The labeling process involved reverse transcription of total RNA into double-stranded cDNA, followed by synthesis of cRNA labeled with Cyanine-3-CTP (Cy3). After hybridization of labeled cRNA with the chips, we used the Agilent Scanner G2505C (Agilent Technologies) for scanning to obtain raw images. In the data processing phase, we employed the Feature Extraction software (version 10.7.1.1, Agilent Technologies) to process the raw images and extract data. Subsequently, we performed quantile normalization on the raw data to ensure data consistency. Following normalization, we filtered the data, ensuring that at least 75% of probes from each group of samples were detected, and these retained probes were used for subsequent comparison and analysis. In essence, our study culminated in a comprehensive exploration of gene expression dynamics, regulatory RNA elements, and their potential roles in the context of HGC-27 cells under the influence of OMT intervention. This was an in vitro study with two experimental groups: HGC-27 cells treated with 2.64 mg/mL oxidized sophoridine alkaloid (OMT) for 48 hours (intervention group) Untreated HGC-27 cells (control group) Each group had 3 biological replicates for a total of 6 samples. Comprehensive RNA expression profiling was performed on all samples using the Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188). Total RNA quality and integrity were assessed before labeling and hybridization to the microarray chips. Raw image data was processed and normalized before statistical comparisons between the intervention and control groups were made to identify differentially expressed mRNAs, lncRNAs, and circRNAs.