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Sample GSM34442 Query DataSets for GSM34442
Status Public on Nov 23, 2005
Title A1-01-Right-Lung
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 Autopsy patient #1 lung metastasis from breast
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: -0.17335459
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 A1 Lung Met
Intrinsic pair:pair 4. 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 Nov 17, 2017
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 -2.659 22575 279 43 47 13 107 93 51 32 806 120 35 75 286 45 -2.54 .47 0 Y -2.659
2 .75 22470 55 9 47 10 66 36 50 33 500 80 35 46 8 14 .459 .08 0 Y .75
3 -.317 22365 89 16 47 9 105 53 54 35 710 120 38 73 51 41 -.264 .38 0 N -.317
4 -.597 22260 866 224 49 77 768 323 62 190 774 156 43 540 934 617 -.718 .92 0 N -.597
5 -.593 22155 381 80 49 76 364 144 59 157 775 156 41 256 390 259 -.626 .85 0 N -.593
6 .404 22050 60 11 47 38 75 39 53 82 503 80 37 52 14 19 .207 .16 0 Y .404
7 -2.984 21945 323 39 47 62 107 48 54 222 746 120 38 75 340 42 -2.9 .54 0 Y -2.984
8 .058 21840 720 140 47 14 970 227 56 66 695 120 39 683 768 800 -.063 .94 0 N .058
9 .052 21735 357 61 47 12 498 153 56 49 739 120 39 350 363 376 .004 .88 0 N .052
10 .685 21630 69 12 47 17 104 46 53 37 510 80 37 73 26 42 .71 .25 0 N .685
11 -.079 21525 98 18 47 42 125 62 51 76 709 120 35 88 63 59 .055 .86 0 N -.079
12 1.819 21420 162 31 47 40 620 206 51 73 810 156 35 436 136 480 1.802 .8 0 N 1.819
13 .228 21315 74 10 47 10 99 46 53 33 516 80 37 69 32 38 .245 .32 0 N .228
14 -3.466 21210 390 76 47 16 101 50 54 51 798 156 38 71 422 38 -3.381 .41 0 Y -3.466
15 -.49 21105 1777 373 49 10 1596 489 54 31 779 156 38 1123 1934 1377 -.671 .95 0 N -.49
16 -.183 21000 174 89 48 10 219 86 53 37 741 120 37 154 154 135 -.106 .79 0 N -.183
17 .193 20895 71 11 47 12 92 45 53 43 494 80 37 64 28 32 .17 .29 0 N .193
18 .168 20790 299 33 46 17 447 133 53 67 720 120 37 314 297 334 .131 .9 0 N .168
19 -.186 20685 829 184 47 18 946 330 53 83 851 156 37 666 891 783 -.315 .94 0 Y -.186
20 -.02 20580 64 13 47 15 73 39 51 39 472 80 35 51 19 19 -.088 .54 0 N -.02

Total number of rows: 22575

Table truncated, full table size 1862 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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