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Sample GSM34499 Query DataSets for GSM34499
Status Public on Jun 05, 2007
Title BC00053
Sample type RNA
 
Channel 1
Source name Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Organism Homo sapiens
Characteristics reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Extracted molecule total RNA
Extraction protocol Total RNA isolated by Stratagene.
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name Breast Tumor
Organism Homo sapiens
Characteristics age: 71
er (1=positive; 0=negative): 0
pgr (1=positive; 0=negative): 0
her2 clinical status ihc/fish (1=positive; 0=negative): 1
node status (1=positive=1 or more nodes+; 0=negative): 1
grade: 3
size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin): 2
rfs event (0=no relapse, 1=relapsed at any site or died of disease): 1
rfs months: 27
overall survival event (0=alive, 1=dod or doc): 1
overall suvival months: 28
pam50 predictions plus claudin-low classification (cell line predictor): Normal
dscores unc337: -0.074100939
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.
Description Age: 71, ER status: negative, Node status: positive, grade: 3, Size: 2 to 5cm, RFS event: relapsed or died of disease, RFS months: 27, Overall survival event: DOD or DOC, Overall survival months: 28, Single Sample Predictor Subtype: Normal Breast-like
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Nov 02, 2004
Last update date Jul 17, 2015
Contact name Charles M. Perou
E-mail(s) cperou@med.unc.edu
Organization name University of North Carolina at Chapel Hill
Department Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
Street address 12-044 Lineberger Comprehensive Cancer Center CB# 7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7264
Country USA
 
Platform ID GPL887
Series (11)
GSE1992 A New Breast Tumor Intrinsic Gene List Identifies Novel Characteristics that are Conserved Across Microarray Platforms
GSE2607 Biological Classification of Breast Cancer by Real-Time Quantitative RTPCR: Comparisons to Microarray and Histopathology
GSE2740 Estrogen-regulated genes predict survival in estrogen receptor and/or progesterone receptor-positive breast cancers

Data table header descriptions
ID_REF Agilent probe reference IDs
VALUE same as UNF_VALUE but with flagged values removed
SPOT spot number on array
CH1_MEAN channel 1 mean intensity
CH1_SD standard deviation of channel 1 intensity
CH1_BKD_MEDIAN channel 1 background median intensity
CH1_BKD_SD standard deviation of channel 1 background median intensity
CH2_MEAN channel 2 mean intensity
CH2_SD standard deviation of channel 2 intensity
CH2_BKD_MEDIAN channel 2 background median intensity
CH2_BKD_SD standard deviation of channel 2 background median intensity
TOT_BPIX number of background pixels
TOT_SPIX number of spot pixels
CH2BN_MEDIAN channel 2 normalized background median intensity
CH2IN_MEAN channel 2 normalized mean intensity
CH1DL_MEAN channel 1 Lowess_normalized mean intensity
CH2DL_MEAN channel 2 Lowess_normalized mean intensity
LOG_RAT2N_MEAN log2_ratio of (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots
CONTROL Y: control gene; N: not control
UNF_VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN

Data table
ID_REF VALUE SPOT CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_SD CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_SD TOT_BPIX TOT_SPIX CH2BN_MEDIAN CH2IN_MEAN CH1DL_MEAN CH2DL_MEAN LOG_RAT2N_MEAN CORR FLAG CONTROL UNF_VALUE
1 -3.555 22575 448 95 38 6 91 44 50 25 832 120 42 77 444 37 -3.556 .43 0 Y -3.555
2 .599 22470 46 7 38 6 66 30 51 25 508 80 43 56 8 13 .7 .17 0 Y .599
3 .086 22365 69 12 38 5 103 49 50 27 731 120 42 88 39 41 .569 .48 0 N .086
4 -1.282 22260 843 132 38 5 352 115 51 27 726 120 43 300 767 315 -1.648 .9 0 N -1.282
5 -.862 22155 427 73 38 6 269 88 52 27 768 120 44 229 391 215 -1.071 .87 0 N -.862
6 .8 22050 47 8 40 7 71 31 56 30 336 52 47 60 7 13 .893 .23 0 Y .8
7 -4.28 21945 449 96 38 6 77 33 50 26 744 120 42 65 464 23 -4.158 .29 0 Y -4.28
8 .587 21840 636 103 38 6 816 180 49 26 638 120 41 697 552 830 .134 .97 0 N .587
9 .188 21735 305 52 38 6 361 106 52 24 637 120 44 308 269 306 -.016 .91 0 N .188
10 .711 21630 56 9 39 8 96 42 52 27 708 120 44 82 21 34 1.16 .41 0 N .711
11 -.253 21525 77 11 38 5 103 47 51 25 725 120 43 88 49 41 .207 .46 0 N -.253
12 1.102 21420 88 15 38 7 200 77 52 27 743 120 44 170 58 126 1.333 .75 0 N 1.102
13 .38 21315 54 8 39 9 83 37 54 30 320 52 46 70 18 23 .678 .29 0 N .38
14 -3.794 21210 488 114 38 6 88 40 50 26 756 120 42 75 487 35 -3.776 .45 0 Y -3.794
15 -1.203 21105 2390 333 38 6 845 177 50 26 710 120 42 722 2075 901 -1.791 .97 0 N -1.203
16 .038 21000 112 22 37 5 156 64 51 25 714 120 43 133 87 89 .263 .76 0 N .038
17 .154 20895 51 7 37 5 74 37 52 26 496 80 44 63 16 18 .44 .27 0 N .154
18 1.486 20790 159 28 37 6 414 130 50 24 768 120 42 353 125 352 1.35 .92 0 N 1.486
19 .708 20685 603 120 37 6 842 205 51 26 665 120 43 719 523 855 .256 .96 0 Y .708
20 .359 20580 52 8 38 6 77 40 51 26 494 80 43 65 16 21 .652 .26 0 N .359

Total number of rows: 22575

Table truncated, full table size 1826 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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