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| 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
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| 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.
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| 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.
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| Contributor(s) |
Tang Y, Jiao S |
| Citation(s) |
32589942 |
| Submission date |
Jul 30, 2019 |
| Last update date |
Sep 06, 2020 |
| Contact name |
yang tang |
| E-mail(s) |
tangyang2013@sibcb.ac.cn
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| Organization name |
Shanghai Institute of Biochemistry and Cell Biology
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| Street address |
Yueyang Road 320
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| City |
shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA557376 |
| SRA |
SRP216828 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135086_SOS_transcript.fpkm.xlsx |
3.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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