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Sample GSM1314330 Query DataSets for GSM1314330
Status Public on Jan 25, 2014
Title C_HP-,s10-12710
Sample type RNA
 
Source name H. pylori-negative FFPE specimen
Organism Homo sapiens
Characteristics disease: H. pylori-negative FFPE specimen (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 (cancerous region), C_HP-,s10-12710
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 3.4933882
A_25_P00010020 25.34633
A_25_P00010021 -1.0306097
A_25_P00010023 4.2940636
A_25_P00010041 -0.40581506
A_25_P00010042 19.79122
A_25_P00010043 -1.933105
A_25_P00010044 -1.583947
A_25_P00010047 673.707
A_25_P00010048 275.15326
A_25_P00010053 1692.3438
A_25_P00010054 540.23517
A_25_P00010062 20.10263
A_25_P00010063 3.366073
A_25_P00010070 5277.214
A_25_P00010071 4231.473
A_25_P00010072 3929.5115
A_25_P00010073 1427.8567
A_25_P00010078 300.81473
A_25_P00010079 103.50964

Total number of rows: 3523

Table truncated, full table size 86 Kbytes.




Supplementary file Size Download File type/resource
GSM1314330_C_HP-_s10-12710.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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