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Sample GSM108707 Query DataSets for GSM108707
Status Public on Oct 20, 2006
Title stroma_normal_reduction_sample101_rep2
Sample type RNA
 
Channel 1
Source Name Stratagene universal human reference
Organism(s) Homo sapiens
Characteristics none
Extracted molecule total RNA
Label Cy5
 
Channel 2
Source Name normal breast stroma from reduction tissue
Organism(s) Homo sapiens
Characteristics LN: NA
ESR: NA
GRADE: NA
Her2: NA
TT: Normal-Connective
PR: NA
AgeOfOperation: 54
TumorSize: NA
MenopauseStatus: Pre-menopause
TypeOfCase: Normal
recurrence: No
cellularity: High
Extracted molecule total RNA
Label Cy3
 
 
Description RNA isolated from laser capture microdissected breast tissue. RNA has undergone two rounds of T7 linear amplification.
Data processing Raw Cy5 and Cy3 intensities were background corrected using the RMA background
correction algorithm. Data was tranformed to log2 ratios and within array normalization
was performed using spatial and intensity-dependent loess. Between array normalization
was performed by scaling the arrays to have the same median absolute deviation.
 
Submission date May 12, 2006
Contact name Greg Finak
E-mail(s) finak@mcb.mcgill.ca
Phone (514)398-7071 x09317
Fax 514 257-8235
URL http://www.mcb.mcgill.ca/~finak/
Organization name McGill University
Department Mcgill Center For Bioinformatics
Lab Hallett, M. Park, M.
Street address 3775 University
City Montreal
State/province QC
ZIP/Postal code H3A2B4
Country Canada
 
Platform ID GPL1708
Series (1)
GSE4823 Comparison of normal breast epithelium and stroma from reduction and I.D.C. cases

Data table header descriptions
ID_REF
VALUE log2 ratio of normalized Cy5 to Cy3 signal
rMeanSignal The average foreground signal in the Cy5 channel
gMeanSignal The average foreground signal in the Cy3 channel
rBGMedianSignal The median background signal in the Cy5 channel
gBGMedianSignal The median background signal in the Cy3 channel

Data table
ID_REF VALUE rMeanSignal gMeanSignal rBGMedianSignal gBGMedianSignal
1 -0.574964999999999 5.808387e+002 5.551935e+002 44 43
2 0.198348999999999 5.220690e+001 1.066897e+002 43.5 42
3 0.821662 1.610714e+002 1.402143e+002 44 43
4 0.670284 1.966207e+002 1.654828e+002 44 42
5 0.475066 4.151724e+002 2.825517e+002 44 43
6 0.588262 1.198966e+002 1.256207e+002 44 43
7 -2.048708 1.213871e+002 2.618710e+002 45 43
8 0.220266000000000 1.193448e+002 1.453448e+002 44 44
9 -0.762093 5.306429e+002 5.472143e+002 43.5 44
10 -0.623500999999999 3.732667e+002 3.782333e+002 44 43
11 -0.0820150000000002 1.174483e+002 1.584483e+002 43 42
12 0.386779000000001 1.956100e+003 1.040767e+003 44 43
13 -2.3413 1.305862e+002 3.006897e+002 44 43
14 -2.302379 1.473000e+002 3.219000e+002 45 43
15 -0.303294 7.027586e+001 1.440690e+002 44 43
16 0.180319 5.278571e+001 1.033214e+002 44 44
17 -0.2885660 2.879655e+002 2.740000e+002 43 44
18 -0.289877000000001 7.224516e+002 5.623548e+002 44 44
19 1.868945 2.314533e+003 5.070333e+002 44 44
20 4.948864 1.212968e+003 1.513871e+002 44 43

Total number of rows: 43931

Table truncated, full table size 2244 Kbytes.




Supplementary data files not provided
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