|
| Status |
Public on Dec 20, 2011 |
| Title |
Control MO DMSO Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Injection of control MO at 1-4 cell stage. DMSO exposure at 48 hpf. RNA sampled at 52 hpf.
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tupfel/Long fin mutation wild-type strain (TL)
tissue: pooled embryos
developmental stage: 52 hpf
|
| Treatment protocol |
Embryos at the 1-4 cell stage were injected with 3-5 nl of a control morpholino (MO) or gene-specific MO to knockdown Nrf2a, Nrf2b, or a Nrf2a+b combination. At 48 hpf, triplicate groups of 5 embryos were exposed to 2 µM of tert butyl hydroquinone or 2% DSMO for 4 hours.
|
| Growth protocol |
Zebrafish (Danio rerio) from the Tupfel/Long fin mutation wild-type strain (TL) were used in all experiments. Fish were maintained and embryos were collected under standard light and temperature conditions as previously described.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 52 hpf, embryos were fixed in RNA Later and stored at -80°C. RNA was extracted using RNA STAT-60, following the manufacturer's instruction.
|
| Label |
Cy3
|
| Label protocol |
The RNA samples were labeled with Cy3 using the Agilent Low Input Quick Amp Labeling kit, following the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Cy3 labeled samples were hybridized to the Agilent 4x44K zebrafish microarray at the Genome Technology Core of the Whitehead Institute (Cambridge, MA), following the Agilent protocols.
|
| Scan protocol |
Hybridization results were scanned using a Agilent DNA Micorarray Scanner.
|
| Description |
Gene expression with control MO, DMSO exposure at 48 hpf. RNA sampled at 52 hpf
|
| Data processing |
Raw array data obtained from the Whitehead Institute were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative). Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed.
|
| |
|
| Submission date |
Oct 04, 2011 |
| Last update date |
Dec 20, 2011 |
| Contact name |
Andrew G. McArthur |
| E-mail(s) |
mcarthua@mcmaster.ca
|
| Organization name |
McMaster University
|
| Department |
Biochemistry & Biomedical Sciences
|
| Street address |
1280 Main Street West
|
| City |
Hamilton |
| State/province |
Ontario |
| ZIP/Postal code |
L8S 4K1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14664 |
| Series (1) |
| GSE32594 |
Nrf2b: a novel zebrafish paralog of the oxidant-responsive transcription factor Nrf2. |
|
