|
| Status |
Public on Jan 01, 2013 |
| Title |
CONTROL-3 |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish embryo control
|
| Organism |
Danio rerio |
| Characteristics |
treatment: control
tissue: whole embryo
|
| Biomaterial provider |
Zebrafish (Danio rerio) embryos were obtained by natural mating and raised in embryo water from an on-site culture at the Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Spain.
|
| Treatment protocol |
Zebrafish embryos from the control treatment
|
| Growth protocol |
At the time of sample collection, fish were humanely killed in a buffered (200 mg Na2HCO3/L) solution tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond WA, USA). Tissue was transferred to a labeled microcentrifuge tube and snap-frozen in liquid nitrogen, then stored at -80o C until extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Total RNA was stored at -80oC until analyzed.
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA).
|
| |
|
| Hybridization protocol |
The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.
|
| Scan protocol |
An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.
|
| Description |
Data were resolved from microarray images using Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA).
|
| Data processing |
Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.
|
| |
|
| Submission date |
Jul 06, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Natalia Vinas |
| E-mail(s) |
natalia@icnanotox.org, nataliarv@gmail.com
|
| Phone |
6016343764
|
| Organization name |
Mississippi State University
|
| Street address |
3909 Halls Ferry Rd
|
| City |
Vicksburg |
| State/province |
MS |
| ZIP/Postal code |
39180 |
| Country |
USA |
| |
|
| Platform ID |
GPL6457 |
| Series (1) |
| GSE39169 |
Environmentally relevant concentrations of the flame retardant BDE-209 in sediment cause minimal effects on Zebrafish embryos. |
|
