|
| Status |
Public on Sep 21, 2013 |
| Title |
Radio-resistant nasopharyngeal carcinoma patient NO.60 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Radio-resistant nasopharyngeal carcinoma patient tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Radio-resistant nasopharyngeal carcinoma tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was reverse transcribed using the Superscript III RNase H- Reverse Transcriptase kit (Invitrogen) following the manufacturer’s instructions with Cy3-dUTP for NPCI or Cy5-dUTP for NPC.
|
| |
|
| Channel 2 |
| Source name |
Nasopharyngeal chronic inflammation patient tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasopharyngeal chronic inflammation tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was reverse transcribed using the Superscript III RNase H- Reverse Transcriptase kit (Invitrogen) following the manufacturer’s instructions with Cy3-dUTP for NPCI or Cy5-dUTP for NPC.
|
| |
|
| |
| Hybridization protocol |
The probe was dissolved in 20 µl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide]. Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml denatured salmon sperm DNA at 42C for 6 hrs. Fluorescent probe mixtures were denatured at 90C for 5 minutes, and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42C for 15-17 hours. Next, the hybridized chips were each washed at 60C for 10 min in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC, then dried at room temperature.
|
| Scan protocol |
The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA) at two wavelengths, 635nm and 532 nm, to detect emission from both Cy5 and Cy3 respectively.
|
| Description |
RR-NPC 3
Radio-resistant nasopharyngeal carcinoma patient tissue before treatment.
|
| Data processing |
The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP. Ratios of Cy5 to Cy3 were computed using the GenePix Pro 3.0 median of ratio method. Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged 'Bad' or 'Not Found' by GenePix software was removed from the final data. Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were selected from each array and used for further analysis.
|
| |
|
| Submission date |
Sep 26, 2011 |
| Last update date |
Sep 21, 2013 |
| Contact name |
shu yang |
| E-mail(s) |
yangshu_zfb@yahoo.cn
|
| Organization name |
Fudan University
|
| Street address |
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science
|
| City |
shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL4381 |
| Series (1) |
| GSE32389 |
Nasopharyngeal carcinoma patient samples: radio-sensitive samples vs. radio-resistant samples |
|
