|
| Status |
Public on Jun 01, 2012 |
| Title |
Control Fish Replicate2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole fish 7 day post-fertilization
|
| Organism |
Danio rerio |
| Characteristics |
condition: Developing fish maintained in egg water (with 0.05% ethanol as vehicle)
|
| Treatment protocol |
Developing zebrafish were exposed to 500, 1500 and 4500 µg/L BPA for 7 days from 3 hour post-fertilization onwards groups of four zebrafishes. All control fish were maintained in egg water with 0.05% ethanol (vehicle).
|
| Growth protocol |
Zebrafish were maintained at room temperature (26°C + 1°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, 10 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. Reference RNA was obtained by pooling male and female whole adult total RNA at a ratio of 9:1 respectively. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Whole Fish
|
| Organism |
Danio rerio |
| Characteristics |
reference: Reference RNA was obtained by pooling 9:1 ratio of male and female total RNA extracted from whole adult wild-type zebrafish.
|
| Growth protocol |
Zebrafish were maintained at room temperature (26°C + 1°C)
|
| 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, 10 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. Reference RNA was obtained by pooling male and female whole adult total RNA at a ratio of 9:1 respectively. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| |
| Hybridization protocol |
The respective paired Cy5- labeled cDNAs from control or treated sample and Cy3-labeled cDNAs from reference samples were co-hybridized on a single array at 42°C for 16 h in a hybridization chamber (MAUI, USA) on a glass array spotted with 22,776 zebrafish oligo probes.
|
| 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 |
Biological replicate 2 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)
|
| Data processing |
The data were global median normalized. Normalized ratio of means defined by CH1/CH2
|
| |
|
| Submission date |
Jun 30, 2010 |
| Last update date |
Jun 01, 2012 |
| Contact name |
Siew Hong Lam |
| E-mail(s) |
[email protected]
|
| 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 |
GPL10182 |
| Series (1) |
| GSE22634 |
Zebrafish toxicogenomics and phenotypic analyses reveal molecular insights into bisphenol-A (BPA) early-life exposure toxicity. |
|
