|
| Status |
Public on Mar 09, 2010 |
| Title |
HONE1_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
epithelial biopsies of carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nasopharynx
cell line: HONE1
disease state: carcinoma
|
| Growth protocol |
The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. The NP460hTert cells were maintained in culture medium as previously described (H.M. Li et al., 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with RNeasy mini kit (Qiagen) according to the manufacturer’s introduction. The integrity of the RNA samples was verified using the RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
The Agilent’s low RNA input linear amplification / one-color labeling kit were used for target preparation essentially followed the protocol recommended by Agilent Technologies. Briefly, 1000 ng of total RNA was reverse transcribed into cDNA using the T7 promoter primer. Cyanine 3-dCTP labeled cRNA was synthesized from the cDNA by using the T7 RNA polymerase. To remove unincorporated nucleotides, the labeled cRNA was purified using the RNeasy mini kit (Qiagen).
|
| |
|
| Hybridization protocol |
Array hybridization was performed in 100 ul of a hybridization mixture containing cRNA probes at 65℃ for 17 hrs.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent G2565BA DNA microarray scanner using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of HONE1, biological replicate 1 of 2.
|
| Data processing |
Fluorescence intensities of spots were quantified, background subtracted, and dye normalized by Feature Extraction software, version 8.1.1 (Agilent Technologies). The data were then imported and analyzed using GeneSpring GX (Agilent Technologies) to generate gene lists of differentially expressed (change in expression with fold change > 2).
|
| |
|
| Submission date |
Mar 10, 2009 |
| Last update date |
Mar 09, 2010 |
| Contact name |
Chia Huei Lee |
| E-mail(s) |
chlee124@nhri.edu.tw
|
| Organization name |
Taiwan National Health Research Institute
|
| Department |
National Institute of Cancer Research
|
| Street address |
35, Keyan Rd.
|
| City |
Zhunan Miaoli County |
| ZIP/Postal code |
114 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE15170 |
Expression profiling of nasopharyngeal carcinoma cell lines |
| GSE15191 |
Nasopharyngeal carcinoma cell lines TW01 and HONE1: transcriptomic and genomic analyses |
|
