NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM34423 Query DataSets for GSM34423
Status Public on Jun 05, 2007
Title PB138-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): 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: -0.111825553
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 15 of PB138. 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) 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 (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 -1.848 22575 185 52 36 7 133 95 63 44 917 156 42 89 193 53 -1.667 .45 0 Y -1.848
2 -.58 22470 113 66 36 13 157 341 62 49 811 156 41 105 104 69 -.267 .52 0 Y -.58
3 -.326 22365 171 130 36 9 217 119 62 45 802 156 41 145 161 129 -.377 .69 0 N -.326
4 -1.514 22260 1175 201 35 8 490 186 61 44 795 156 40 328 1181 413 -1.983 .89 0 N -1.514
5 -.753 22155 487 91 36 7 376 125 64 46 732 120 42 252 486 288 -1.102 .85 0 N -.753
6 1.205 22050 56 8 36 5 174 74 62 43 663 120 41 116 31 71 1.907 .56 0 Y 1.205
7 -2.061 21945 158 23 36 5 122 68 67 46 680 120 44 81 167 40 -1.723 .31 0 Y -2.061
8 1.17 21840 613 102 37 6 1423 396 67 48 711 120 44 955 589 1325 .662 .96 0 N 1.17
9 1.279 21735 265 51 37 7 713 249 70 47 730 120 46 478 245 596 .922 .92 0 N 1.279
10 .439 21630 56 8 43 11 120 61 78 58 206 32 52 80 20 27 1.107 .29 0 N .439
11 -.654 21525 79 12 37 7 128 71 65 63 745 120 43 85 64 41 0 .37 0 N -.654
12 1.516 21420 128 26 38 10 413 158 66 46 790 156 44 277 104 298 1.372 .85 0 N 1.516
13 -.012 21315 60 8 39 266 128 86 76 1740 466 80 51 85 33 32 .695 .98 0 N -.012
14 -3.05 21210 168 28 38 211 103 58 70 1382 740 120 46 69 188 22 -2.498 .2 0 Y -3.05
15 -1.594 21105 2164 442 39 10 775 235 65 45 773 156 43 520 2134 706 -2.158 .94 0 N -1.594
16 .241 21000 105 14 38 8 202 100 64 42 674 120 42 135 88 104 .473 .68 0 N .241
17 .02 20895 60 10 38 7 120 62 64 44 501 80 42 80 34 35 .788 .31 0 N .02
18 1.585 20790 116 20 37 7 394 136 66 43 846 156 44 264 92 278 1.478 .87 0 N 1.585
19 -.277 20685 846 156 37 7 776 230 65 50 697 120 43 520 834 689 -.761 .93 0 Y -.277
20 1.084 20580 52 6 39 8 134 78 66 59 310 52 44 89 20 43 1.792 .23 0 N 1.084

Total number of rows: 22575

Table truncated, full table size 1851 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap