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Transcriptome profiling of over-expression of GC0643 in HGC-27 cancer cells

ABSTRACT: Transcriptome profiling of over-expression of GC0643 in HGC-27 cancer cells

PROVIDER: PRJNA857285 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20068121_1.fastq.gz	Fastqsanger.gz
	SRR20068121_2.fastq.gz	Fastqsanger.gz
	SRR20068122_1.fastq.gz	Fastqsanger.gz
	SRR20068122_2.fastq.gz	Fastqsanger.gz
	SRR20068123_1.fastq.gz	Fastqsanger.gz

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Transcriptome profiling of over-expression of GC0643 in HGC-27 cancer cells

Project description:To investigate the molecular biological function of GC0643, we enforced GC0643 overexpression in HGC-27 cell lines.

2022-10-12 | GSE207820 | GEO

Transcriptome analysis of HGC-27 after infection with Sendai virus

Project description:To better understand the interactions between Hippo signaling and antiviral signaling at transcription level, a high-throughput RNA-seq technology was utilized in gastric cancer cells HGC-27 at 48 hours after Sendai virus (SeV) infection.

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Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with SHAP or control peptide

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.

2020-06-05 | GSE135086 | GEO

Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with siSTRN3 mixture or negative control siRNA

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.

2020-06-05 | GSE135085 | GEO

Effect of overexpssion Kallistatin(SERPINA4) in HGC-27 cell line

Project description:Kallistatin has been demonstrated to possess inhibitory effects across several malignancies, including hepatocellular carcinoma, gastric cancer and breast cancer. Subsequent evidence has increasingly suggested that KS has pleiotropic roles in modulating a broad spectrum of diseases, including in diabetic nephropathy, idiopathic pulmonary fibrosis and autoimmune uveitis. However, the precise function and molecular mechanisms underlying tumor-induced immune escape attributed to KS remain unclear, necessitating further investigation to determine its role in this context.For this propose, we establish SERPINA4 stably expressed cell line(and control) in HGC-27 cells, and RNA-seq was performed to reveal the trancriptome changes between there two cell lines.

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HGC-RACK1

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2016-03-01 | E-MTAB-3484 | biostudies-arrayexpress

Transcriptomes analyses of gastric cancer HGC-27 cell line treated with lactate

Project description:Transcriptomes analyses of gastric cancer HGC-27 cell line treated with lactate

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Transcriptome analysis of HGC-27 after infection with Sendai virus

Project description:Transcriptome analysis of HGC-27 after infection with Sendai virus

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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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Pull-down of nuclear proteins from HGC-27 cell line

Project description:To identify nuclear proteins that interact with KIT2KIT* G-quadruplex DNA, pull-down assays were performed with nuclear extracts from the KIT-positive HGC-27 cell line. Streptavidin-coated paramagnetic beads were derivatized with the biotinylated oligonucleotide and subsequently incubated with nuclear extracts. Bound proteins were eluted with a KCl gradient. A last fraction was obtained by boiling beads in denaturing Laemmli sample loading buffer. When solved by SDS-PAGE, this last fraction exhibited three main bands that were cut and subjected to in-gel trypsin digestion and LC-MSE analyses for protein identification. Two of them (bands S1 and S2 at ~15 kDa and ~28 kDa, respectively) corresponded to Streptavidin monomer and dimer that detached from the beads along boiling procedure. That aside, the band at ~50 kDa (band V) was associated to the intermediate filament protein Vimentin.

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