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Sample GSM374626 Query DataSets for GSM374626
Status Public on May 06, 2009
Title Dog Normal mammary gland 7
Sample type RNA
 
Channel 1
Source name Normal mammary gland
Organism Canis lupus familiaris
Characteristics disease state: normal tissue
tissue: mammary gland
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with RNAzolB and finally dissolved in RNase-free water. Then 25μg of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA was dissolved in RNase-free water to a final concentration of 0.2 μg/μl.
Label Cy5
Label protocol cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 μg of total RNA and labelled with Cy5 or Cy3 (Cy Dye, Amersham Pharmacia Biotech).
 
Channel 2
Source name Normal reference pool
Organism Canis lupus familiaris
Characteristics sample: Pool of normal samples
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with RNAzolB and finally dissolved in RNase-free water. Then 25μg of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA was dissolved in RNase-free water to a final concentration of 0.2 μg/μl.
Label Cy3
Label protocol cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 μg of total RNA and labelled with Cy5 or Cy3 (Cy Dye, Amersham Pharmacia Biotech).
 
 
Hybridization protocol 5 μg of labelled-RNA from each sample were co-hybridized with 5 μg of a normal reference pool, consisting of an equal amount of cRNA extracted from mammary healthy samples. Labelled cRNAs were fragmented to an average size of 50-100 nucleotides by heating the samples to 60°C with 10mM of zinc chloride and then adding an hybridization buffer containing 1M NaCl, 0.5% sodium sarcosine, 50mM MES, pH6.5, and formamide to a final concentration of 30%. The final volume was 3ml at 40°C.
Scan protocol Slides were washed and scanned using a confocal laser scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.1).
Description Normal mammary gland
Data processing Lowess normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Rosetta Resolver gene expression analysis software (version 3.2, Rosetta Biosoftware, Seattle, WA) was used.
 
Submission date Feb 25, 2009
Last update date May 05, 2010
Contact name Paolo Uva
Organization name IRCCS Istituto Giannina Gaslini
Lab Clinical Bioinformatics
Street address Via Gerolamo Gaslini, 5
City Genoa
ZIP/Postal code 16147
Country Italy
 
Platform ID GPL7198
Series (1)
GSE14999 Gene expression profiling of human and dog breast cancers

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) of dye-swapped pairs representing test/reference.
AvgIntensity Corrected average log intensity of channels
Intensity1 Cy3 intensity (Ch2)
Intensity2 Cy5 intensity (Ch1)
Pvalue P-value of LogRatio

Data table
ID_REF VALUE AvgIntensity Intensity1 Intensity2 Pvalue
10025854541 0.067386806 -0.535761178 0.270639986 0.315025002 0.239987969
10025854543 -0.010184086 0.953466058 9.09862518 8.89765549 0.832057059
10025854544 -0.174459323 -0.949589014 0.138929993 0.094755001 0.079797529
10025854547 -0.092707492 0.047001313 1.24048996 1.00242996 0.04496599
10025854564 -0.003285794 -0.838942826 0.145884991 0.144605011 0.946586549
10025854570 0.023674393 -0.89226079 0.132510006 0.140520006 0.627794921
10025854576 -0.133048609 0.614279866 4.79960012 3.53379488 0.00323984
10025854583 -0.04176116 -1.27922511 0.060449999 0.055155002 0.475195467
10025854584 -0.030782092 0.858521223 7.48176003 6.97114515 0.496736944
10025854585 -0.775900662 -0.664137959 0.565265 0.086549997 3.28E-06
10025854593 0.25035581 1.12125015 9.93515587 17.8748951 7.66E-05
10025854594 0.031127904 0.759771109 5.56814957 5.97184467 0.523689806
10025854608 3.35E-05 0.022574671 1.05337501 1.05352497 0.99940002
10025854620 -0.031731408 0.102758393 1.31480503 1.22281003 0.600165427
10025854621 0.021366924 -1.00679255 0.097290002 0.103505 0.734854519
10025854623 0.216999993 1.49513233 24.3569107 40.146019 0.092788644
10025854630 1.35081768 0.798237085 1.33454001 30.044281 3.68E-36
10025854633 -0.122549556 0.24968873 2.05045009 1.54649997 0.005834712
10025854634 -0.261033684 1.02602291 14.4604397 7.89828968 1.15E-06
10025854638 0.220658317 -0.446291625 0.277074993 0.464100003 0.003481174

Total number of rows: 39558

Table truncated, full table size 2730 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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