|
Status |
Public on Sep 01, 2008 |
Title |
white muscle tissue individu 433al |
Sample type |
RNA |
|
|
Source name |
white muscle tissue
|
Organism |
Coregonus clupeaformis |
Characteristics |
hybrid 433 male
|
Extracted molecule |
total RNA |
Extraction protocol |
Dissected white muscle tissue (250-350 mg) was sampled for 65 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 |
Alexa 647
|
Label protocol |
Reverse transcriptase PCR was performed using 15 μg of total RNA per sample following the SuperScriptä II Reverse Transcriptase protocol (Invitrogen life technologies). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).
|
|
|
Hybridization protocol |
following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).
|
Scan protocol |
The transcript levels inferred from fluorescent labels were quantified by scanning microarrays using a ScanArray Express scanner (Packard Bioscience).
|
Description |
Spot location and quantification was done with the QuantArray© (Perkin Elmer) software, retaining the mean intensity value for each spot.
|
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, 2,255 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.
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|
|
Submission date |
Mar 24, 2008 |
Last update date |
May 27, 2008 |
Contact name |
Nicolas Derome |
E-mail(s) |
nicolas.derome@bio.ulaval.ca
|
Phone |
1 (418) 656 7726
|
Fax |
1 (418) 656 2043
|
Organization name |
Université LAVAL
|
Department |
Biologie
|
Lab |
Derome
|
Street address |
Av de la médecine
|
City |
Québec |
State/province |
QC |
ZIP/Postal code |
G1V0A6 |
Country |
Canada |
|
|
Platform ID |
GPL6260 |
Series (1) |
GSE11378 |
eQTL mapping in Lake Whitefish Species Pairs. |
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