|
| Status |
Public on Dec 01, 2015 |
| Title |
18740_FD-pCDH.txt:gProcessedSignal(normalized) |
| Sample type |
RNA |
| |
|
| Source name |
FaDu_pCDH vector
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: FaDu
cell type: Head and neck cell line
transfected with: pCDH vector (control)
|
| Treatment protocol |
FaDu cells were infection with pCDH-ARID3B or empty vector control.
|
| Growth protocol |
cultivated in RPMI + 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.
|
| Label |
CY3-CTP
|
| Label protocol |
0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.
|
| |
|
| Hybridization protocol |
Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3
|
| Description |
18740_FD-pCDH.txt:gProcessedSignal(raw)
|
| Data processing |
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
Normalized signal is generated from gProcessedSignal after normalized by quantile
There are three kinds of flags for the data quality of the feature (gFEFlags):
Detected: the data quality of the feature is good enough. In general, the signal of the feature is well above background, uniform, not saturated, and not a population outlier.
Compromise: the data quality of the feature is also good but the signal is too weak because of the low expression level of the gene. Generally, the signal of the feature is uniform, not saturated not a population outlier, but not well above background.
not Detected: the data quality of the feature Generally not good enough. the signal of the feature maybe not uniform, or saturated or a population outlier.
|
| |
|
| Submission date |
Mar 06, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Tsai-Tsen Liao |
| Phone |
+886-228235870
|
| Organization name |
Institute of Clinical Medicine
|
| Lab |
Dr. M.H. Yang's Lab
|
| Street address |
No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C
|
| City |
Taipei |
| State/province |
State... |
| ZIP/Postal code |
11221 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE66602 |
The mRNA expression of FaDu-Ctrl, FaDu-ARID3B cells |
| GSE66603 |
let-7 controls cancer stemness through ARID3B |
|
| Relations |
| Reanalyzed by |
GSE113533 |
