|
| Status |
Public on Jun 19, 2009 |
| Title |
12M2L |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Liver from male fathead minnow exposed to a field site
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: liver
exposure: field site 12
|
| Biomaterial provider |
Fish were exposed by the University of Minnesota. RNA was extracted at the University of Florida.
|
| Treatment protocol |
Fathead minnow liver exposed in vivo for 48h to field site 12
|
| Growth protocol |
To conduct the field exposures at each field site, FHM were transported from the laboratory to the field site in aerated, insulated tanks. At each site, 25 males and 25 females were placed in separate wire mesh minnow traps with the entrance funnel plugged. The traps were anchored to the bottom in the stream current with the top of the traps submerged. Fish were removed from the traps 48 h later and transported back to the laboratory in aerated, insulated tanks containing the stream water. Immediately upon arrival at the laboratory, four males and four females were sacrificed as described for the laboratory exposures. Liver and gonads were removed and stored in liquid nitrogen until processed for arrays. All procedures involving live fish were reviewed and approved by the University of Minnesota Institutional Animal Care and Use Committee (IACUC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
Cy5
|
| Label protocol |
cDNA synthesis, cRNA labeling, 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
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: liver, brain, and gonad from control fathead minnow females and males
|
| Biomaterial provider |
University of Florida
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, cRNA labeling, 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) was used.
|
| Scan protocol |
The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA).
|
| Description |
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 log 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 |
Jun 16, 2009 |
| Last update date |
Jun 18, 2009 |
| 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) |
| GSE16645 |
Site-specific impacts on gene expression and behavior in fathead minnows exposed to streams adjacent to STPs |
|
