|
| Status |
Public on Oct 28, 2005 |
| Title |
ZFL T1+ |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Zebrafish liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
Zebrafish liver tumor tissue or normal liver tissue
|
| Growth protocol |
Zebrafish were reared at room temperature (27 ± 2°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
|
| Label |
Cy5
|
| Label protocol |
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Zebrafish normal liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
Reference RNA was obtained by pooling equal amount of male total RNA extracted from liver tissues of wild-type zebrafish.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
|
| Label |
Cy3
|
| Label protocol |
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| |
| Scan protocol |
The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
|
| Description |
Zebrafish liver tumor tissue (induced by carcinogens) vs zebrafish normal liver tissue.
|
| Data processing |
Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2
|
| |
|
| Submission date |
Oct 27, 2005 |
| Last update date |
Oct 27, 2005 |
| Contact name |
Siew Hong Lam |
| E-mail(s) |
dbslsh@nus.edu.sg
|
| Phone |
(65)- 68742860
|
| Fax |
(65)-67792486
|
| Organization name |
National University of Singapore
|
| Department |
Biological Sciences
|
| Street address |
14 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL2715 |
| Series (1) |
| GSE3519 |
Molecular Conservation of Zebrafish and Human Liver Tumors. |
|
| Data table header descriptions |
| ID_REF |
Unique ID |
| VALUE |
log2 of PRE_VALUE |
| CH1_Median |
CH1(F635) median fluorescence intensity |
| CH1_MEAN |
CH1 (F635) mean fluorescence intensity |
| CH1_SD |
CH1 (F635) fluorescence intensity standard deviation |
| CH1_BKD_Median |
CH1 (F635) background median fluorescence intensity |
| CH1_BKD_MEAN |
CH1 (F635) background mean fluorescence intensity |
| CH1_BKD_SD |
CH1 (F635) background fluorescence intensity standard deviation |
| %>CH1_BKD_+2SD |
% of feature pixels greater than two standard deviations over the background |
| CH2_Median |
CH2(F532) median fluorescence intensity |
| CH2_MEAN |
CH2 (F532) mean fluorescence intensity |
| CH2_SD |
CH2 (F532) fluorescence intensity standard deviation |
| CH2_BKD_Median |
CH2 (F532) background median fluorescence intensity |
| CH2_BKD_MEAN |
CH2 (F532) background mean fluorescence intensity |
| CH2_BKD_SD |
CH2 (F532) background fluorescence intensity standard deviation |
| %>CH2_BKD_+2SD |
% of feature pixels greater than two standard deviations over the background |
| Ratio_of_Means |
Unnormalized ratio of means defined by CH1/CH2 |
| AREA |
Number of feature pixels |
| BKD_AREA |
Number of feature background pixels |
| CH1_Median-CH1_BKD |
Channel 1 median signal |
| CH2_Median-CH2_BKD |
Channel 2 median signal |
| CH1_Mean-CH1_BKD |
Channel 1 mean signal |
| CH2_Mean-CH2_BKD |
Channel 2 mean signal |
| PRE_VALUE |
Normalized ratio of means defined by CH1/CH2 |
