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Sample GSM277011 Query DataSets for GSM277011
Status Public on Sep 01, 2008
Title white muscle tissue individu 352al
Sample type RNA
 
Source name white muscle tissue
Organism Coregonus clupeaformis
Characteristics hybrid 352
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.
 
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.

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

Data table
ID_REF VALUE
14 10.2155474661224
20 10.6480661605503
27 13.4139299095755
29 10.1397963442661
44 14.1575545311266
64 12.1485169597332
69 10.5973306296055
70 10.0250266704649
71 11.0711743689112
86 13.1728696844449
97 12.2107212841795
100 12.2316149425
106 11.9425384292422
119 10.4177222469907
129 10.6982313475316
135 11.9867899285637
136 10.3259062449003
142 11.0348997656093
151 13.6809144313731
155 11.2292845004514

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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