GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE135085 Query DataSets for GSE135085
Status Public on Jun 05, 2020
Title Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with siSTRN3 mixture or negative control siRNA
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design Total mRNA was extracted from HGC-27 cells treated with siSTRN3 mixture or negative control siRNA in triplicate. 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 (6)
GSM3985179 HGC-27 siNC_1
GSM3985180 HGC-27 siNC_2
GSM3985181 HGC-27 siNC_3
BioProject PRJNA557377
SRA SRP216827

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135085_siSTRN3_transcript.fpkm.xlsx 4.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap