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

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

PROVIDER: PRJNA557377 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9860870_1.fastq.gz	Fastqsanger.gz
	SRR9860870_2.fastq.gz	Fastqsanger.gz
	SRR9860871_1.fastq.gz	Fastqsanger.gz
	SRR9860871_2.fastq.gz	Fastqsanger.gz
	SRR9860872_1.fastq.gz	Fastqsanger.gz

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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

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

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

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

| PRJNA826822 | ENA

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.

2018-01-09 | GSE107096 | GEO

Whole transcriptomes analyses of HGC-27 cell line treated with control DMSO, disulfiram, thiram or CX-6258

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.

2024-06-12 | GSE168618 | GEO

Transcriptomes analyses of AARS1 knockdown HGC-27 cells treated with lactate

Project description:Transcriptomes analyses of AARS1 knockdown HGC-27 cells treated with lactate

| PRJNA826823 | ENA

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.

2022-04-04 | PXD026505 | Pride

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.

2024-10-01 | GSE262922 | GEO

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

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

| PRJNA557376 | ENA