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Sample GSM276837 Query DataSets for GSM276837
Status Public on Sep 01, 2008
Title white muscle tissue individu 288al
Sample type RNA
 
Source name white muscle tissue
Organism Coregonus clupeaformis
Characteristics hybrid 288
female
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.
 
Submission date Mar 21, 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.

Data table header descriptions
ID_REF
VALUE R-lowess normalized, log2-transformed signal intensities

Data table
ID_REF VALUE
14 9.40622384363876
20 10.5486637871554
27 12.4672883182620
29 9.6054579173185
44 14.0503049443165
64 12.1069225483932
69 10.4523149715782
70 9.54732758267845
71 10.7863614132964
86 13.3855462747001
97 11.8661159039594
100 11.7911022072770
106 12.4269063735540
119 9.57918079762656
129 10.7283289876512
135 11.8187836633838
136 9.7515617381964
142 10.7773142448075
151 12.3381006405615
155 10.5992382909469

Total number of rows: 2255

Table truncated, full table size 48 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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