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Sample GSM1314340 Query DataSets for GSM1314340
Status Public on Jan 25, 2014
Title N_HP-,S07-28675
Sample type RNA
 
Source name H. pylori-negative FFPE specimen
Organism Homo sapiens
Characteristics disease: H. pylori-negative FFPE specimen (non-cancerous region)
tissue: FFPE specimen
Treatment protocol All subjects of this study received gastroscopy for gastric cancer screening and conformation of histological gastric adenocarcinoma diagnosis.
Growth protocol Sixteen gastric cancer patients matched for age, sex and H. pylori status, who received curative operation at Seoul National University Bundang Hospital, were included for microarray study.
Extracted molecule total RNA
Extraction protocol After manual dissection under microscopic guidance avoiding the contamination of inflammatory cells and stromal cells, H&E stained sections 50 μm in thickness from cancerous and non-cancerous regions of intestinal type of gastric cancer FFPE samples were reviewed by one pathologist (H.S.L). Each section was incubated in xylene and total RNA was extracted using a RecoverAllTM Total Nucleic Acid Isolation kit (Life Technologies, CA, USA).
Label Cy3
Label protocol 400 ng of total RNA was labeled with cyanine 3-pCp using the Agilent miRNA Complete Labeling kit and hybridized to the array according to the manufacturer’s protocol.
 
Hybridization protocol After purification, labeled samples were resuspended with Gene Expression Blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s Human miRNA Microarray (60K, Release 16.0) and hybridized at 55 °C for 20 h with 20 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).
Scan protocol The hybridization images were analyzed by Agilent DNA microarray Scanner.
Description miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,S07-28675
Data processing Feature Extraction software (version 10.10.1.1) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. Background intensity and feature nonuniform outliers were removed by standard procedures. Data visualization and analysis were performed with GeneSpring GX (version 7.3) software (Agilent Technologies). Signal cut-off measurements were less than 5, and normalized to 75th percentile of signal intensity to standardize each chip for cross-array comparison. Differentially expressed miRNAs were identified using a Student’s two-sample t-test with p values cut off by 0.05 and fold change more than 2.0. One-way ANOVO was used to analyze the correlation between the expression levels of miRNAs and clinic-pathological features of the patients.
 
Submission date Jan 24, 2014
Last update date Jan 25, 2014
Contact name Jung Min Kim
E-mail(s) jmkim2010@korea.com
Phone 82-10-3459-4776
Organization name NAR Center, Inc. & Genoplan, Inc.
Department Department of Health Genomics
Lab Genetics & Genomics
Street address Gangnam-gu Teheran-ro 216
City Seoul
ZIP/Postal code 06221
Country South Korea
 
Platform ID GPL15159
Series (1)
GSE54397 microRNA expressions in gastric cancer

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_25_P00010019 14.74381
A_25_P00010020 -0.41060024
A_25_P00010021 -0.045368254
A_25_P00010023 1.5733933
A_25_P00010041 0.08570194
A_25_P00010042 -1.6831778
A_25_P00010043 -2.3005462
A_25_P00010044 -3.5046134
A_25_P00010047 330.28482
A_25_P00010048 81.50844
A_25_P00010053 2237.9165
A_25_P00010054 565.29425
A_25_P00010062 2.3574052
A_25_P00010063 0.4954193
A_25_P00010070 9951.31
A_25_P00010071 7737.4517
A_25_P00010072 5237.7314
A_25_P00010073 1754.2806
A_25_P00010078 141.6192
A_25_P00010079 45.992058

Total number of rows: 3523

Table truncated, full table size 86 Kbytes.




Supplementary file Size Download File type/resource
GSM1314340_N_HP-_S07-28675.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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