|
| Status |
Public on Jan 17, 2017 |
| Title |
Control Replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Liver tissue exposed to solvent control
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: Liver
Sex: male
treatment: solvent control
|
| Treatment protocol |
Exposed to estrogen EE2, a mixture of EE2 and the anti-estrogen ZM, or solvent control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from FHM livers with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
Cy5
|
| Label protocol |
Array hybridizations were performed using a reference design and Agilent standard protocol. The liver samples were labeled with Cy5, while the reference sample was labeled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
Reference sample
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: Pool of liver, gonad, and brain
Sex: Pooled male and female
|
| Treatment protocol |
Exposed to estrogen EE2, a mixture of EE2 and the anti-estrogen ZM, or solvent control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from FHM livers with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).
|
| Label |
Cy3
|
| Label protocol |
Array hybridizations were performed using a reference design and Agilent standard protocol. The liver samples were labeled with Cy5, while the reference sample was labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed following the standard Agilent protocol.
|
| Scan protocol |
Arrays were scanned with Agilent scanner.
|
| Description |
TEG-18
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.
|
| Data processing |
Microarray image processing and data pre-processing were performed using Agilent’s Feature Extraction software v 9.5. In brief, log2 transformed signal ratio between the experimental channel and the reference channel was calculated for each spot, followed by within-array LOWESS transformation and between array scale normalization on median intensities (Zahurak, 2007). Two-way ANOVA was performed on the log2 transformed signal ratios of each probe individually, followed by Tukey-HSD pair-wise comparisons to determine genes whose expression was significantly regulated by the treatments.
|
| |
|
| Submission date |
Jan 16, 2017 |
| Last update date |
Jan 17, 2017 |
| 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) |
| GSE93663 |
Fathead minnow liver samples: control, EE2 and EE2/zm |
|
