|
| Status |
Public on May 15, 2013 |
| Title |
Patient 44T |
| Sample type |
RNA |
| |
|
| Source name |
primary lung tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary lung tumor
histology: AD
stage: IV
sex: Male
age: 60 years
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from tumors and normal lung tissues using TRIzol reagent (Invitrogen), and cleaned up RNA with RNeasy mini kit (Qiagen) and RNase-free DNase set (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).
|
| |
|
| Hybridization protocol |
HOA v4.2 arrays (Phalanx Biotech Group, Taiwan) were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 10 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.
|
| Scan protocol |
The arrays were scanned by Axon GenePix 4000B scanner (635nm power 33 PMT 460; 532nm power 33, PMT 460) and quantify the fluoresence intensity.
|
| Description |
Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1087 experimental control probes).
|
| Data processing |
All signal intensities was combined together and processed background subtraction by Microsoft Excel 9.0 software. Keep those probes that flags of GenePix have to be equal to 0 and the signal/noise ratio should be more than 5 for further Quantile normalization developed from Matlab 7.3.
|
| |
|
| Submission date |
May 20, 2010 |
| Last update date |
May 16, 2013 |
| Contact name |
Yi-Ching Wang |
| E-mail(s) |
[email protected]
|
| Phone |
+886-6-2353535
|
| Organization name |
National Cheng Kung University
|
| Department |
Department of Pharmacology, College of Medicine
|
| Street address |
No.1, University Road, Tainan 70101, Taiwan, R. O. C.
|
| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6254 |
| Series (1) |
| GSE21933 |
Gene expression profiles of tumor and paired normal lung tissues from primary non-small cell lung cancer (NSCLC) patients in Taiwan. |
|
