|
| Status |
Public on Dec 22, 2009 |
| Title |
fhm_ovary_hal_61953 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
fhm ovary, exposed to 50 ug haloperidol/L for 96 h
|
| Organism |
Pimephales promelas |
| Characteristics |
gender: female
age: 6 months
tissue: gonad
sample: 61953
|
| Biomaterial provider |
on site culture unit at US EPA, Duluth, MN, USA
|
| Treatment protocol |
Samples for microarray analysis were generated in a 96 h, continuous flow-through experiment. Nominal treatment concentrations for the microarray experiment were 0 and 50 μg haloperidol/L. Chemical (or control water) delivery was initiated 24 h prior to adding fish to the tanks. To start the experiment, fathead minnows (4 males, 4 females per tank) were added to each of three tanks per treatment group. The time of fish addition was staggered by replicate within each treatment such that all samples from a given exposure tank could be collected within 60 min of the intended 96 h exposure duration. After 96 h, fish were anesthetized in buffered MS-222 and weighed. Whole gonads were removed, weighed, and preserved in RNAlater. Samples were stored at -20oC until extracted and analyzed.
|
| Growth protocol |
25 degrees C. 16:8 light:dark photoperiod. Fed frozen Artremia twice daily to satiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from fathead minnow ovary samples using RNeasy kits (Qiagen). RNA quality was assessed with a Agilent 2100 Bioanalyzer and quantity was determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
|
| 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 |
gender: Male and female
tissues: Gonad, liver, brain
|
| 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 |
Sample 61953 - ovary from fathead minnow exposed to 50 ug haloperidol/L for 96 h.
Mention of trade names or commercial products does not constitute endorsement or recommendation for use.
|
| 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 |
Mar 04, 2009 |
| Last update date |
Dec 22, 2009 |
| Contact name |
Daniel L. Villeneuve |
| E-mail(s) |
[email protected]
|
| Organization name |
US EPA
|
| Department |
Mid-Continent Ecology Division
|
| Lab |
National Health and Environmental Effects Research Laboratory
|
| Street address |
6201 Congdon Blvd
|
| City |
Duluth |
| State/province |
MN |
| ZIP/Postal code |
55804 |
| Country |
USA |
| |
|
| Platform ID |
GPL7282 |
| Series (2) |
| GSE15115 |
Small fish comp tox FHM haloperidol 96 h ovary |
| GSE15216 |
Effects of haloperidol on zebrafish and fathead minnow gene expression |
|
