|
| Status |
Public on Nov 25, 2009 |
| Title |
fry_EURO_R5(2)_USR_Y1(2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole fry prior to exogenous feeding
|
| Organism |
Salmo salar |
| Characteristics |
strain: EURO
family: R5
|
| Growth protocol |
Eggs were fertilized and reared at a hatchery; samples were collected as fry prior to any exogenous feeding
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3,Cy5
|
| Label protocol |
Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).
|
| |
|
| Channel 2 |
| Source name |
whole fry prior to exogenous feeding
|
| Organism |
Salmo salar |
| Characteristics |
strain: USR
family: Y1
|
| Growth protocol |
Eggs were fertilized and reared at a hatchery; samples were collected as fry prior to any exogenous feeding
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5,Cy3
|
| Label protocol |
Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).
|
| |
|
| |
| Hybridization protocol |
Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).
|
| Scan protocol |
Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 65). The otsu quantification method within TIGR Spotfinder was used to quantify the scanned microarray files. Integrated intensities were corrected for background and any spots with expression levels < 2 standard deviations above background were removed.
|
| Description |
none
|
| Data processing |
TIGR Microarray Data Analysis System (MIDAS) was used to average dye-swap technical replicates and Limma in R was used to apply a locally weighted linear regression (LOWESS) normalization module. Missing values were imputed with the K-nearest neighbours method using K = 10. The normalized log 2 ratios from the merged dye swaps represent the ratio of the average of (ch1, slide 1 and ch2, slide2)/(ch2, slide1 and ch1, slide 2).
|
| |
|
| Submission date |
Nov 19, 2009 |
| Last update date |
Nov 24, 2009 |
| Contact name |
Wendy Tymchuk |
| E-mail(s) |
[email protected]
|
| Phone |
604-666-7909
|
| Fax |
604-666-3497
|
| Organization name |
Fisheries & Oceans Canada
|
| Department |
Science
|
| Lab |
CAER
|
| Street address |
4160 Marine Drive
|
| City |
West Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V7V1N6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2716 |
| Series (2) |
| GSE19111 |
Conservation genomics of Atlantic salmon (Year One) |
| GSE19170 |
Conservation genomics of Atlantic salmon |
|
