Whole transcriptomes analyses of HGC-27 cell line treated with control DMSO, disulfiram, thiram or CX-6258
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PROVIDER: PRJNA713189 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: To figure out the molecular function of disulfiram, thiram and CX-6258, RNA sequencing was performed to analyze the geome-wide change of disulfiram, thiram and CX-6258 treated HGC-27 cells compared to those of control DMSO treated cells. Methods: Total mRNA was extracted from HGC-27 cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusion: The results showed disulfiram, thiram and CX-6258 may target distinct combinations of various pathways including Hippo pathway. The Hippo signaling indeed can be targeted by disulfiram, thiram and CX-6258 even though these compounds also interfere with other biological processes.
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Project description:Purpose: To explore the molecular mechanisms of SHAP peptide (also termed as SOS) regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of SHAP treated HGC-27 cells compared to those of control peptide cells. Methods: Total mRNA was extracted from HGC-27 cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of SHAP regulating Hippo pathway in gastric cancer.
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Project description:Purpose: To explore the molecular mechanisms of STRN3 regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of siSTRN3 treated HGC-27 cells compared to those of control cells. Methods: Total mRNA was extracted from HGC-27 cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of STRN3 regulating Hippo pathway in gastric cancer.
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Project description: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.
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| PRJNA1094913 | ENA