|
| Status |
Public on Mar 01, 2014 |
| Title |
Patient 1_005T |
| Sample type |
RNA |
| |
|
| Source name |
Advanced gastric carcinoma patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Gastric tumor
ebv: EBV+
histology: CLR
lauren type: Diffuse
age: 53
Sex: M
tumor stage: IIB
her2+: -
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissue by using RNeasy Mini Kit (Qiagen, Hilden, Germany). Quantity and quality of isolated RNA were measured by Nanodrop ND-1000 (Thermo Scientific, Waltham, MA).
|
| Label |
Cy3
|
| Label protocol |
See the manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf). Briefly, total RNA was converted to ds cDNA1 using One-Color Spike Mix. complementary RNA was amplified with T7 promtoer primers and cyanine 3-CTP. Amplified cRNA was purified with Qiagen’s RNeasy mini spin columns and quantified using NanoDrop ND-1000 (Thermo Scientific).
|
| |
|
| Hybridization protocol |
Fragmented cyanine 3-labeled cRNA were loaded on to the gasket slide for hybridization and incubated at 65℃, 10 rpm for 17 hours, See manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf) for detail
|
| Scan protocol |
Microarray slides were scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent). Gene expression data analysis was subsequently conducted in R-project (build 2.11.1). The raw data were normalized by using Quantile method. Paired t-test using Algorithm Limma were performed to select differentially expressed genes (DEG) between normal and tumor tissues in EBV(+)GC and EBV(-)GC. DEGs were clustered based by Cluster 3.0 and Tree View software.
|
| |
|
| Submission date |
Oct 23, 2013 |
| Last update date |
Mar 01, 2014 |
| Contact name |
Charny Park |
| E-mail(s) |
charn78@ncc.re.kr
|
| Organization name |
National Cancer Center
|
| Street address |
323 Ilsan-ro,
|
| City |
Goyaongsi |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
10408 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE51575 |
mRNA Expression Profiling in EBV-postive Gastric Carcinoma and EBV-negative GC in comparison with their normal mucosa tissue |
|
