|
| Status |
Public on Sep 01, 2008 |
| Title |
Whitefish backcross individual 333 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from whole whitefish brains
|
| Organism |
Coregonus clupeaformis |
| Characteristics |
Whitefish backcross individual 333
|
| Treatment protocol |
Brains were dissected from whole frozen fish kept at -80deg.C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected brain tissue (250-350 mg) was sampled for 55 individuals from the hybrid x dwarf backcross mapping family, and stored at - 80°C until RNA extraction. RNA was extracted according to the Trizol Reagent protocol (Gibco BRL) and quantified with a GeneQuant spectrometer (Pharmacia), and RNA integrity was verified with a 2100 Bioanalyzer (Agilent).
|
| Label |
Cy3,Alexa
|
| Label protocol |
Reverse transcriptase PCR was performed using 15 μg of total RNA per sample following the SuperScript II Reverse Transcriptase protocol (Invitrogen life technologies). 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/cbr/grasp/ (Genisphere Array 50 Protocol).
|
| Scan protocol |
Scanned with a ScanArray Express scanner (Packard Bioscience).
Spot location and quantification (mean intensity for each spot) was performed with QuantArray© (Perkin Elmer).
|
| Description |
One of backcross individuals used in analysis. Data from each channel were averaged to obtain normalized score shown in data matrix
|
| Data processing |
Aberrant spot signals were removed before analysis and their values were estimated using the “K-Nearest Neighbors Imputer” function implemented in SAM software (Tusher et al 2001). Genes with intensity less than the mean of the empty spot controls plus 2.5 times their standard deviation were removed from the analysis. According to this criterion, 3,563 among the 16,006 transcripts passed this threshold and were considered for subsequent analyses. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (Kerr et al. 2000), available at: http://www.jax.org/staff/churchill/labsite/software/Rmaanova.
|
| |
|
| Submission date |
Jul 10, 2008 |
| Last update date |
Jul 10, 2008 |
| Contact name |
Andrew R Whiteley |
| E-mail(s) |
[email protected]
|
| Organization name |
Universite Laval
|
| Department |
Biologie
|
| Street address |
Pavillon Marchand
|
| City |
Quebec |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2716 |
| Series (1) |
| GSE12068 |
Brain eQTL analysis of lake whitefish species-pairs (Coregonus sp.) |
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