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Sample GSM34507 Query DataSets for GSM34507
Status Public on Jun 05, 2007
Title PB412-Int
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: --
er (1=positive; 0=negative): --
pgr (1=positive; 0=negative): --
her2 clinical status ihc/fish (1=positive; 0=negative): 0
node status (1=positive=1 or more nodes+; 0=negative): --
grade: --
size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin): --
rfs event (0=no relapse, 1=relapsed at any site or died of disease): --
rfs months: --
overall survival event (0=alive, 1=dod or doc): --
overall suvival months: --
pam50 predictions plus claudin-low classification (cell line predictor): Basal
dscores unc337: -0.202063014
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 Intrinsic pair:pair 19 of PB412. Single Sample Predictor Subtype: Basal-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) [email protected]
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 (9)
GSE1992 A New Breast Tumor Intrinsic Gene List Identifies Novel Characteristics that are Conserved Across Microarray Platforms
GSE2740 Estrogen-regulated genes predict survival in estrogen receptor and/or progesterone receptor-positive breast cancers
GSE2741 Breast Tumor's study

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 -1.789 22575 151 40 34 5 87 49 50 24 978 156 48 84 122 35 -1.699 .39 0 Y -1.789
2 .01 22470 45 5 34 5 63 28 50 26 550 80 48 61 11 11 .241 .03 0 Y .01
3 .772 22365 71 15 34 4 124 55 50 27 814 156 48 120 40 68 .961 .64 0 N .772
4 -.811 22260 935 333 34 4 440 177 50 27 765 156 48 427 785 447 -1.248 .92 0 N -.811
5 -.183 22155 313 108 34 4 263 112 52 26 806 156 50 255 258 227 -.444 .88 0 N -.183
6 .477 22050 47 6 34 14 76 34 52 28 384 52 50 73 14 20 .823 .27 0 Y .477
7 -2.45 21945 152 46 34 6 78 38 53 28 804 156 51 75 126 23 -2.3 .33 0 Y -2.45
8 2.146 21840 463 151 34 4 1459 501 52 27 736 156 50 1416 369 1634 1.671 .97 0 N 2.146
9 1.041 21735 205 68 34 4 356 156 51 26 731 156 49 345 159 327 .792 .9 0 N 1.041
10 .243 21630 55 9 34 5 84 37 50 27 700 120 48 81 24 29 .652 .25 0 N .243
11 -.419 21525 66 12 34 4 82 41 50 26 781 156 48 79 36 27 -.045 .38 0 N -.419
12 2.664 21420 78 17 34 5 321 122 52 26 787 156 50 311 43 273 2.569 .86 0 N 2.664
13 -.081 21315 54 12 34 6 79 42 53 27 418 80 51 76 23 22 .322 .28 0 N -.081
14 -2.342 21210 160 51 34 5 81 38 53 26 760 156 51 78 133 26 -2.224 .38 0 Y -2.342
15 -.874 21105 1388 491 34 4 596 261 51 25 759 156 49 578 1163 634 -1.355 .95 0 N -.874
16 .369 21000 96 25 34 5 136 62 51 25 773 156 49 132 63 82 .421 .69 0 N .369
17 -.265 20895 49 6 34 5 67 33 51 25 507 80 49 65 16 14 .094 .22 0 N -.265
18 1.205 20790 123 36 34 13 242 108 50 25 838 156 48 234 86 198 1.064 .85 0 N 1.205
19 -.097 20685 560 217 34 4 437 198 50 25 816 156 48 424 466 436 -.484 .92 0 Y -.097
20 -.076 20580 48 6 34 5 65 32 48 25 503 80 46 63 15 15 .28 .17 0 N -.076

Total number of rows: 22575

Table truncated, full table size 1803 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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