|
| Status |
Public on Dec 23, 2008 |
| Title |
Trenbolone_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fathead minnow ovary exposed to trenbolone
|
| Organism |
Pimephales promelas |
| Characteristics |
RNA from fathead minnow ovary exposed to 0.5 ug/L trenbolone
|
| Biomaterial provider |
Fish were exposed at EPA (Duluth). RNA was extracted at University of Florida
|
| Treatment protocol |
Fathead minnow ovary exposed for 48h to trenbolone, flutamide, a mix of tronbolone/flutamide or 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 Pool
|
| Organism |
Pimephales promelas |
| Characteristics |
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
|
| Biomaterial provider |
University of Florida
|
| Treatment protocol |
Control fish
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 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 |
Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)
|
| Description |
Biological replicate 1 of 4 trenbolone treated fish
|
| Data processing |
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5. The intensity of each spot was summarized by the median pixel intensity. A log10 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 |
Dec 22, 2008 |
| Last update date |
Dec 29, 2008 |
| Contact name |
Natalia Vinas |
| E-mail(s) |
[email protected], [email protected]
|
| 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) |
| GSE14100 |
Effects of trenbolone, flutamide and a mix of both in fathead minnow ovaries |
|
