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Sample GSM277067 Query DataSets for GSM277067
Status Public on Sep 01, 2008
Title white muscle tissue individu 436al
Sample type RNA
 
Source name white muscle tissue
Organism Coregonus clupeaformis
Characteristics hybrid 436
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 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 9.36078057961155
20 9.15039881163666
27 11.2588641465253
29 9.30227691442645
44 12.6863547271199
64 9.65800207745309
69 9.28840585597755
70 9.30502843511764
71 9.07758321236522
86 11.7043727078952
97 10.1001187032201
100 10.0264323237254
106 10.1490442062213
119 9.31631924773161
129 9.23363861638314
135 11.0832028977619
136 9.26391626520368
142 9.85459934929392
151 11.4467551507505
155 9.40375269526816

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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