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Sample GSM1248655 Query DataSets for GSM1248655
Status Public on Mar 01, 2014
Title Patient 22_104T
Sample type RNA
 
Source name Advanced gastric carcinoma patient
Organism Homo sapiens
Characteristics tissue: Gastric tumor
ebv: EBV+
histology: CA
lauren type: Mixed
age: 52
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 8.901008328
5 7.652563165
6 6.245506999
7 12.27925704
9 5.280949469
10 5.563247242
11 5.163745083
12 10.34811724
13 9.755975346
15 11.50697972
16 4.087922574
17 5.850490021
19 4.662300924
20 9.538893191
21 9.580688151
24 7.994806008
25 8.916915879
26 11.60402545
27 4.386440979
28 8.16675268

Total number of rows: 42735

Table truncated, full table size 737 Kbytes.




Supplementary file Size Download File type/resource
GSM1248655_104_+_T.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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