|
| Status |
Public on Jan 25, 2014 |
| Title |
C_HP-,s07-33646 |
| 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-,s07-33646
|
| 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 |
|
