|
| Status |
Public on Nov 01, 2008 |
| Title |
jaw_vehicle control_4h_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
jaw, vehicle, 4h
|
| Organism |
Danio rerio |
| Characteristics |
AB wild-type strain
|
| Treatment protocol |
AB larvae zebrafish were exposed to TCDD (1 ng/ml; TCDD > 99% purity; Chemsyn, Lenexa, KS) or vehicle [0.1% dimethyl sulfoxide (DMSO)] at 96 hpf for 1 h in water and rinsed with fish water. Treatment conditions were limited to 10 embryos or fewer per 1 ml treatment volume. Larvae were raised in 100-mm Petri dishes containing fish water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Jaws were microdissected as previously described (Javidan and Schilling, 2004). Larvae were anesthetized with Tricaine-S (Aquatic EcoSystems, Apopka, FL), positioned onto a microscope slide and a drop of Lebovitz’s L15 media + 10% fetal bovine serum (Invitrogen, Carlsbad, CA) was placed onto each specimen. With fine forceps (Fine Science Tools, Foster City, CA) the head (anterior of the pectoral fin) was detached from the body then the eyes and brain tissues were removed. Dissected jaws were placed into a microcentrifuge tube and immediately put into a dry ice bucket. Jaws were stored at -80°C.
|
| Label |
biotin
|
| Label protocol |
The One-Cycle Target Labeling and Control Reagents kit was used to synthesize cDNA and biotinylated cRNA following the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA (15 µg) was fragmented and hybridized onto Affymetrix Zebrafish Genechip Arrays following the protocol in the Affymetrix Genechip Expression Analysis Technical Manual.
|
| Scan protocol |
Following hybdrization, the arrays were washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400 using the protocol EukGE WS2v4. Arrays were scanned with an Agilent Gene Array Scanner.
|
| Description |
no additional information
|
| Data processing |
Analysis of the relative abundance of each gene transcript was determined using Arrayassist microarray software (Stratagene, La Jolla, CA). In brief, .CHP files were uploaded into the software and probe intensities were corrected for background noise and normalized across all array replicates with the GC-Robust Multi-Array Average (GC-RMA) algorithm. Expression levels for each transcript were log2-transformed, and the average log2 value for the TCDD samples was compared to the average value for the DMSO replicates. Those transcripts that were altered by TCDD by at least 2 fold over DMSO at any of the time points (p < 0.05) were selected for further analysis. Significant changes were determined by an unpaired t-test.
|
| |
|
| Submission date |
Jun 26, 2008 |
| Last update date |
Jun 27, 2008 |
| Contact name |
Kong M Xiong |
| Organization name |
University of Wisconsin at Madison
|
| Department |
Biomolecular Chemistry
|
| Lab |
Heideman/Peterson Fish Group
|
| Street address |
777 Highland Ave, 5208 Rennebohm Hall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE11893 |
AHR Activation by TCDD Downregulates Sox9b Expression Producing Jaw Malformation in Zebrafish Embryos |
|
