|
| Status |
Public on Jun 01, 2013 |
| Title |
NP Replicate1 48 Hour Female |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Female zebrafish liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
gender: female
sample type: Nitrophenol-treated liver tissue
tissue: liver
treatment: Nitrophenol
time: 48h
|
| Treatment protocol |
Female zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.
|
| 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 equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Male and female zebrafish liver tissue
|
| Organism |
Danio rerio |
| Characteristics |
gender: male and female
tissue: liver
treatment: untreated
sample type: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.
|
| Treatment protocol |
Female zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.
|
| 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 equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| |
| Hybridization protocol |
Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_16.5K_oligo_COMP_v3Apx 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 1 of 3: chloroaniline-treated at 48 Hr
|
| Data processing |
The data were global median normalized. Normalized ratio of means defined by CH1/CH2
|
| |
|
| Submission date |
Jun 17, 2011 |
| Last update date |
Jun 01, 2013 |
| Contact name |
Choong Yong UNG |
| E-mail(s) |
matucy@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Department of Biological Sciences
|
| Street address |
14 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL2715 |
| Series (1) |
| GSE30060 |
Toxicogenomics and phenotypic characterization of adult female zebrafish liver treated with nitrophenol |
|
