Transcriptome analysis of HGC-27 after infection with Sendai virus
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE107096 | GEO | 2018/01/09
SECONDARY ACCESSION(S): PRJNA418982
REPOSITORIES: GEO
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Project description:Transcriptome analysis of HGC-27 after infection with Sendai virus
| PRJNA418982 | ENA
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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: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:Oligonucleotide microarrays were used to establish a profile for gene expression in wild-type airway epithelial cells after paramyxoviral infection. Analysis was performed on mRNA isolated from SeV-infected primary-culture mouse tracheal epithelial cells that were maintained under physiologic conditions (air-liquid interface). Experiment Overall Design: Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions. Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Cultures were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) in the apical compartment for 1 h at 37 °C. Air-liquid-interface conditions were re-established by washing the membrane with PBS. Each culture well was subjected to one of two treatments (SeV, or UV-SeV) for 1 day. N = 4 SeV wells, N = 6 UV-SeV wells, with each well independently analyzed by microarray. No technical replicates were performed, but arrays were evaluated for quality control using the SimpleAffy package (Miller CJ, 2004) in Bioconductor 2.0.
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Project description:Thus, mouse macrophage cultures were established from PBMCs isolated from wild-type control mice and were inoculated with SeV (Sendai virus) or UV-SeV (UV-inactivated SeV). These microarrays were performed in concert with assays of CCL5 and CCR5 expression, viral replication, and cellular apoptosis. Initial experiments indicated that wild-type mouse macrophages inoculated with SeV exhibit induction of CCL5 mRNA to the highest level of any known mouse gene product, while mRNA levels for CCL5 receptors (CCR5 as well as CCR3 and CCR1) or alternative ligands for these receptors (CCL3 and CCL4) were relatively unchanged by viral infection. Keywords: Treatment Comparison
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Project description:Thus, mouse macrophage cultures were established from PBMCs isolated from wild-type control mice and were inoculated with SeV (Sendai virus) or UV-SeV (UV-inactivated SeV). These microarrays were performed in concert with assays of CCL5 and CCR5 expression, viral replication, and cellular apoptosis. Initial experiments indicated that wild-type mouse macrophages inoculated with SeV exhibit induction of CCL5 mRNA to the highest level of any known mouse gene product, while mRNA levels for CCL5 receptors (CCR5 as well as CCR3 and CCR1) or alternative ligands for these receptors (CCL3 and CCL4) were relatively unchanged by viral infection. Experiment Overall Design: Macrophages were pooled from mice and subsequently cultured (~3 mice/well). Each culture well was then subjected to one of two treatments (SeV, or UV-SeV) for 4 days. Thus, per condition, N = 2 culture wells, with each well independently analyzed by microarray. No technical replicates were performed, but arrays were evaluated for quality control using the SimpleAffy package (Miller CJ, 2004) in Bioconductor 1.5.
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