|
| Status |
Public on May 13, 2009 |
| Title |
FAD in vivo - 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fathead minnow ovary exposed to fadrozole
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: ovary
|
| Biomaterial provider |
Fish were exposed at EPA (Duluth). RNA was extracted at University of Florida.
|
| Treatment protocol |
Fathead minnow ovary exposed in vitro for 12h to fadrozole, or solvent control
|
| Growth protocol |
Adult (ca. 6 month old) female FHM from an on-site culture (EPA’s Mid-Continent Ecology Division Laboratory, Duluth) were acclimated to test conditions (25oC, 16:8 light:dark photoperiod, and fed adult brine shrimp twice daily) over a period of one week as described in USEPA (2001). Exposures were initiated by transferring fish from the acclimation tanks to randomly assigned treatment tanks, n = 6 fish per treatment tank. Water quality conditions, monitored daily, were maintained within the guidelines established for fathead minnow reproduction tests.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
CY5
|
| Label protocol |
cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)
|
| |
|
| Channel 2 |
| Source name |
Reference sample
|
| Organism |
Pimephales promelas |
| Characteristics |
sample type: liver, brain, and gonad pool
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
CY3
|
| Label protocol |
cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)
|
| |
|
| |
| Hybridization protocol |
Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)
|
| Scan protocol |
The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA)
|
| Description |
RNA from fathead minnow ovary exposed in vivo to a 50 ug/L fadrozole
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.
|
| Data processing |
The intensity of each spot was summarized by the median pixel intensity. A log2 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.
|
| |
|
| Submission date |
May 01, 2009 |
| Last update date |
May 12, 2009 |
| 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 |
GPL7282 |
| Series (1) |
| GSE15924 |
Fathead minnow ovaries exposed in vivo or in vitro to fadrozole |
|
