|
| Status |
Public on Aug 02, 2006 |
| Title |
CtrXM_24hr.3_m |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Zebrafish liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
Zebrafish liver tissue exposed to arsenic
|
| 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 Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and
resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Zebrafish liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
Reference RNA was obtained by pooling equal amount of male and female 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 and Cy5-dUTP (Amersham Inc.), respectively. 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 |
Fish were treated with arsenic [As(V)] acid (Na2HAsO4.7H2O; Sigma, USA) at 60 mg/L in a static condition for 96 hours (h) whereby less than 10% mortality occurred in arsenic-treated group within the experiment duration. No mortality was observed in the control group. The concentration was chosen based on an initial survival versus concentration experiment. Fish livers were sampled at 8 h, 24 h, 48 h and 96 h, and 12 fish livers were separated into 3 pooled-samples (each pooled samples consist of 4 livers) at each time point.
Three biological replicates are performed for each time point (8,24,48,96 hrs). Test and control samples are hybridized against a reference. No dye swap experiment has been performed.
|
| Data processing |
The data were global median normalized.Normalized ratio of means defined by CH1/CH2
|
| |
|
| Submission date |
Aug 03, 2005 |
| Last update date |
Aug 03, 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) |
| GSE3048 |
Trancriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver. |
|
| 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 |
