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Sample GSM81164 Query DataSets for GSM81164
Status Public on May 01, 2007
Title PB267_Repeat1
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: --
er (1=positive; 0=negative): --
pgr (1=positive; 0=negative): 0
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: -0.240369216
Biomaterial provider Phil Bernard - Utah
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 Exact Replicate of PB232. Single Sample Predictor Subtype: Basal-like
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 (5)
GSE3165 Identification of conserved gene expression features across human and murine mammary tumors
GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors.
GSE10893 Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival

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 -.013 22575 87 27 35 6 115 47 45 16 905 156 34 87 60 60 .027 .79 0 Y -.013
2 .02 22470 89 15 36 6 118 41 45 17 692 120 34 90 61 62 .08 .69 0 Y .02
3 -.075 22365 136 49 36 12 176 76 47 17 785 156 35 134 116 110 -.014 .88 0 N -.075
4 -.412 22260 619 284 36 12 552 266 45 16 739 156 34 421 627 471 -.591 .97 0 N -.412
5 -.777 22155 654 291 35 6 465 216 45 16 762 156 34 354 667 389 -.952 .96 0 N -.777
6 -.007 22050 90 16 36 6 117 44 44 18 694 120 33 89 62 62 .052 .72 0 Y -.007
7 .028 21945 88 17 36 6 117 38 45 17 708 120 34 89 60 61 .081 .73 0 Y .028
8 .714 21840 640 309 36 6 1170 579 44 16 812 156 33 893 643 1056 .51 .96 0 N .714
9 .623 21735 460 89 36 6 797 165 43 16 654 120 32 608 455 701 .441 .97 0 N .623
10 .54 21630 77 22 36 6 126 53 45 17 775 156 34 96 47 69 .596 .78 0 N .54
11 -.102 21525 122 22 36 6 154 55 45 16 676 120 34 117 100 93 -.051 .79 0 N -.102
12 1.925 21420 170 63 36 6 672 283 45 17 781 156 34 512 148 564 1.835 .95 0 N 1.925
13 .125 21315 90 26 36 6 124 49 44 16 719 156 33 94 62 68 .176 .81 0 N .125
14 .061 21210 96 30 36 6 129 52 44 16 738 156 33 98 69 72 .115 .81 0 Y .061
15 -.867 21105 4280 1773 36 6 2669 1122 44 16 724 156 33 2037 4507 2471 -1.083 .98 0 N -.867
16 -.069 21000 138 51 36 6 177 75 45 17 794 156 34 135 118 113 -.014 .89 0 N -.069
17 -.111 20895 98 15 36 6 123 41 45 17 673 120 34 93 72 66 -.071 .75 0 N -.111
18 .124 20790 306 52 35 6 404 103 44 17 691 120 33 308 299 326 .021 .94 0 N .124
19 .424 20685 1339 562 36 6 2011 884 43 16 772 156 32 1535 1382 1855 .205 .98 0 Y .424
20 -.155 20580 95 17 36 6 116 39 44 16 690 120 33 88 68 61 -.102 .73 0 N -.155

Total number of rows: 22575

Table truncated, full table size 1856 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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