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Sample GSM1314343 Query DataSets for GSM1314343
Status Public on Jan 25, 2014
Title N_HP-,S10-18586
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-,S10-18586
Data processing Feature Extraction software (version 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
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
VALUE Normalized signal intensity

Data table
A_25_P00010019 0.30883345
A_25_P00010020 -0.8338579
A_25_P00010021 0.16193406
A_25_P00010023 0.9843686
A_25_P00010041 -2.4178371
A_25_P00010042 -1.9982828
A_25_P00010043 -1.0826019
A_25_P00010044 -1.5421617
A_25_P00010047 198.61314
A_25_P00010048 57.453846
A_25_P00010053 587.0143
A_25_P00010054 192.54735
A_25_P00010062 0.19705774
A_25_P00010063 -0.3195538
A_25_P00010070 3469.2217
A_25_P00010071 3113.0183
A_25_P00010072 2505.649
A_25_P00010073 890.4559
A_25_P00010078 66.75801
A_25_P00010079 24.670544

Total number of rows: 3523

Table truncated, full table size 86 Kbytes.

Supplementary file Size Download File type/resource
GSM1314343_N_HP-_S10-18586.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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