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Sample GSM81186 Query DataSets for GSM81186
Status Public on May 01, 2007
Title BR-02-7043
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
Biomaterial provider Strategene
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: 67
er (1=positive; 0=negative): 1
pgr (1=positive; 0=negative): 1
her2 clinical status ihc/fish (1=positive; 0=negative): 0
node status (1=positive=1 or more nodes+; 0=negative): 0
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): --
rfs months: --
overall survival event (0=alive, 1=dod or doc): --
overall suvival months: --
pam50 predictions plus claudin-low classification (cell line predictor): LumB
dscores unc337: 0.138075248
Biomaterial provider Charles Perou - UNC
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: 67, ER status: positive, Node status: negative, grade: 3, Size: 1 to 2cm, Single Sample Predictor Subtype: LuminalB
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Oct 31, 2005
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 (6)
GSE3165 Identification of conserved gene expression features across human and murine mammary tumors
GSE6130 Agreement in Breast Cancer Classification between Microarray and qRT-PCR from Fresh-Frozen and Formalin-Fixed Tissues
GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors.

Data table header descriptions
ID_REF Spot Reference ID
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 .307 22575 69 20 36 408 52 18 33 29 709 120 33 52 22 27 -.796 .48 0 Y .307
2 -.494 22470 57 15 36 625 36 9 33 93 648 120 33 36 9 6 -2.806 .44 0 Y -.494
3 -.116 22365 79 27 36 259 54 18 33 28 637 120 33 54 31 28 -1.035 .62 0 N -.116
4 -.369 22260 822 405 35 24 824 417 33 8 624 120 33 832 896 694 .021 .98 0 N -.369
5 -.034 22155 582 285 37 898 687 352 33 37 647 120 33 693 604 590 .276 .96 0 N -.034
6 -.091 22050 63 36 36 844 40 11 32 36 663 120 32 40 15 14 -1.756 .89 0 Y -.091
7 .091 21945 68 20 35 49 47 17 32 9 625 120 32 47 21 22 -1.136 .6 0 Y .091
8 .333 21840 655 264 36 137 1046 452 33 9 615 120 33 1056 705 888 .725 .93 0 N .333
9 -.173 21735 330 135 36 128 312 145 33 9 637 120 33 315 304 269 -.06 .92 0 N -.173
10 .56 21630 62 15 36 24 47 15 32 8 636 120 32 47 16 23 -.793 .35 0 N .56
11 .026 21525 90 26 36 14 69 23 32 8 650 120 32 69 44 45 -.546 .73 0 N .026
12 -1.127 21420 130 38 36 16 64 19 32 9 712 120 32 64 81 37 -1.556 .72 0 N -1.127
13 .562 21315 65 19 36 18 52 15 33 10 692 120 33 52 19 28 -.61 .46 0 N .562
14 -.081 21210 72 29 36 18 48 14 33 8 622 120 33 48 23 22 -1.262 .47 0 Y -.081
15 .07 21105 3739 1135 37 23 6654 2357 33 8 636 120 33 6721 4831 5073 .854 .98 0 N .07
16 -.179 21000 116 35 36 22 90 32 33 8 650 120 33 90 71 63 -.488 .75 0 N -.179
17 -1.078 20895 75 45 36 37 39 10 33 18 663 120 33 39 22 10 -2.699 .28 0 N -1.078
18 .187 20790 162 51 35 43 171 71 33 28 558 80 33 172 124 141 .13 .87 0 N .187
19 -.472 20685 1271 598 37 99 1287 622 33 51 640 120 33 1300 1464 1056 .038 .94 0 Y -.472
20 -.437 20580 70 20 36 34 42 12 33 8 640 120 33 42 20 15 -1.916 .31 0 N -.437

Total number of rows: 22575

Table truncated, full table size 1839 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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