|
| Status |
Public on Dec 15, 2009 |
| Title |
Liver harvested at 156 days replicate 3 [compressed] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
liver (control)
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
harvested on which day of the normal photoperiod: Day 0
|
| Treatment protocol |
Post Spawned Female Rainbow Trout over the course of a compressed photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction following the manufacturer's protocol
|
| Label |
Alexa Fluor 555
|
| Label protocol |
Labelled using I\nvitrogen’s Superscript cDNA Indirect Labeling kit and the manufacturer's protocol, and Alexa fluors.
|
| |
|
| Channel 2 |
| Source name |
liver (test)
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
harvested on which day of the normal photoperiod: Day 156
|
| Treatment protocol |
Post Spawned Female Rainbow Trout over the course of a compressed photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction following the manufacturer's protocol
|
| Label |
Alexa Fluor 647
|
| Label protocol |
Labelled using I\nvitrogen’s Superscript cDNA Indirect Labeling kit and the manufacturer's protocol, and Alexa fluors.
|
| |
|
| |
| Hybridization protocol |
Samples were mixed with 20 µg tRNA and 20 µg Herring Sperm DNA to prevent non specific hybridization, then mixed with 35 µl of modified “Genisphere” hybridization buffer (50% formamide, 40% 20x SSC, 9% Denhardt’s solution, 1% SDS). This mixture was then applied to the arrays and allowed to hybridize overnight (16 hr) at 45 o C. After hybridization, arrays were washed in SSC/SDS buffers with descending stringency to remove any unhybridized or weakly (nonspecifically) hybridized cDNA’s.
|
| Scan protocol |
Arrays were scanned using a Perkin Elmer ScanArray Express, with laser power and PMT gain varied to equalize fluorescence intensity between channels and to prevent over saturation of signal intensity.
|
| Description |
Biological replicate 3
|
| Data processing |
Data were extracted using ScanArray Express software (Perkin Elmer). The median fluorescence intensity with background subtracted was imported Genespring microarray analysis software for further analysis. Data were LOWESS normalized and spots that did not meet a minimum signal intensity were removed.
|
| |
|
| Submission date |
Dec 15, 2009 |
| Last update date |
Dec 15, 2009 |
| Contact name |
Sharon E. Hook |
| E-mail(s) |
[email protected]
|
| Phone |
+61 0297106839
|
| Organization name |
CSIRO
|
| Department |
Centre for Environmental Contaminants Research
|
| Street address |
Private Mail Bag 7
|
| City |
Bangor |
| State/province |
NSW |
| ZIP/Postal code |
2234 |
| Country |
Australia |
| |
|
| Platform ID |
GPL2716 |
| Series (1) |
| GSE19478 |
Normal and shortened photoperiods in liver, ovary, and pituitarty |
|
