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Series GSE135086 Query DataSets for GSE135086
Status Public on Jun 05, 2020
Title Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with SHAP or control peptide
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design Total mRNA was extracted from HGC-27 cells treated with SHAP or control peptide. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina NovaSeq 6000.
Contributor(s) Tang Y, Jiao S
Citation(s) 32589942
Submission date Jul 30, 2019
Last update date Sep 06, 2020
Contact name yang tang
Organization name Shanghai Institute of Biochemistry and Cell Biology
Street address Yueyang Road 320
City shanghai
ZIP/Postal code 200031
Country China
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (2)
GSM3985185 HGC-27 Ctrl
GSM3985186 HGC-27 SOS
BioProject PRJNA557376
SRA SRP216828

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE135086_SOS_transcript.fpkm.xlsx 3.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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