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Sample GSM108685 Query DataSets for GSM108685
Status Public on Oct 20, 2006
Title stroma_normal_adjacent_sample047_rep2
Sample type RNA
 
Channel 1
Source name Stratagene universal human reference
Organism Homo sapiens
Characteristics none
Extracted molecule total RNA
Label Cy5
 
Channel 2
Source name histologically normal stroma adjacent to I.D.C.
Organism Homo sapiens
Characteristics LN: Positive
ESR: Positive
GRADE: II
Her2: Positive
TT: Normal-Connective
PR: Positive
AgeOfOperation: 62
TumorSize: 20
MenopauseStatus: Post-menopause
TypeOfCase: Malignant
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
Last update date Jun 13, 2012
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 -0.846903999999999 7.301000e+002 7.914000e+002 48 62
2 -0.785149 6.367857e+001 2.542143e+002 47 61
3 -0.219652 2.840000e+002 3.132333e+002 47 61
4 -0.313444000000000 3.474667e+002 3.561333e+002 48 59
5 0.0613650000000003 6.378966e+002 4.825517e+002 48 62
6 -0.549451 1.845517e+002 2.856207e+002 47 62
7 -2.635607 1.760417e+002 4.711667e+002 47 63
8 -0.631791000000001 2.030714e+002 2.977500e+002 48 62
9 -0.595166000000001 6.893226e+002 6.561935e+002 47 61
10 -0.391241000000001 1.353759e+003 1.145069e+003 47 61
11 -0.505496 2.318333e+002 3.026667e+002 47 61
12 0.260857000000000 3.010571e+003 1.789214e+003 47.5 60
13 0.201518 2.012857e+002 2.482143e+002 47 62
14 -2.555821 1.885862e+002 4.680690e+002 48 61
15 -0.695163 1.262593e+002 2.685556e+002 47 62
16 -0.240267 6.453846e+001 2.158077e+002 47 61
17 -0.364288999999999 5.132333e+002 4.683667e+002 46 60
18 -0.286289999999999 1.167034e+003 9.088276e+002 46 62
19 2.345311 3.495692e+003 6.252692e+002 46 61
20 3.547093 2.401167e+003 3.408000e+002 46 59.5

Total number of rows: 43931

Table truncated, full table size 2272 Kbytes.




Supplementary file Size Download File type/resource
GSM108685_US22502628_251239112401_S01_A01.txt.gz 10.3 Mb (ftp)(http) TXT

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