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Sample GSM373119 Query DataSets for GSM373119
Status Public on Jun 15, 2010
Title 9830-030363B
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 Stratagene
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 A44K11240-2761
Organism Homo sapiens
Characteristics age: 58
er (1=positive; 0=negative): 0
pgr (1=positive; 0=negative): 0
her2 clinical status ihc/fish (1=positive; 0=negative): 1
node status (1=positive=1 or more nodes+; 0=negative): 1
grade: --
size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin): 3
rfs event (0=no relapse, 1=relapsed at any site or died of disease): 0
rfs months: 30
overall survival event (0=alive, 1=dod or doc): 0
overall suvival months: 30
pam50 predictions plus claudin-low classification (cell line predictor): Normal
dscores unc337: -0.08994512
Biomaterial provider UNC and Washington University
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 Tissue: Breast Tumor, Subtype: LumA
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Feb 20, 2009
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 GPL1708
Series (3)
GSE10893 Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival
GSE18229 Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of Breast Cancer
GSE26338 Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse

Data table header descriptions
ID_REF Spot Reference ID
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
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
VALUE same as UNF_VALUE but with flagged values removed
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 LOG_RAT2N_MEAN 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 VALUE CORR FLAG CONTROL UNF_VALUE
1 -4.211 44290 317 84 38 9 63 28 47 21 538 80 41 56 293 15 -4.273 .21 0 Y -4.273
2 -1.262 44084 49 12 37 9 52 23 47 21 419 80 41 46 9 6 -.628 .05 0 Y -.628
3 .275 43878 100 31 38 8 129 55 45 21 369 80 40 115 65 79 .284 .69 0 N .284
4 .45 43672 109 26 38 9 154 65 45 20 404 80 40 137 75 102 .454 .77 0 N .454
5 1.774 43466 272 105 38 9 943 370 46 18 355 80 41 841 238 878 1.88 .97 0 N 1.88
6 .662 43260 104 34 37 9 165 73 46 20 349 80 41 147 70 112 .664 .8 0 N .664
7 -4.322 43054 298 130 38 99 61 25 46 20 354 80 41 54 273 14 -4.259 .3 0 Y -4.259
8 -1.297 42848 64 17 37 9 58 23 45 20 387 80 40 51 26 13 -.962 .08 0 N -.962
9 .045 42642 68 17 37 27 81 31 45 32 343 80 40 72 31 35 .148 .76 0 N .148
10 .341 42436 82 27 37 58 113 48 49 116 339 80 43 100 47 61 .378 .91 0 N .378
11 -.201 42230 61 14 38 17 69 29 46 19 369 80 41 61 22 23 .023 .28 0 Y .023
12 .579 42024 1220 232 37 8 2025 381 46 18 395 80 41 1808 1155 2026 .81 .98 0 N .81
13 .512 41818 91 23 37 9 132 55 45 20 444 80 40 117 56 82 .537 .73 0 N .537
14 -4.083 41612 309 138 37 10 62 23 44 21 349 80 39 55 286 17 -4.07 .28 0 Y -4.07
15 .628 41406 59 15 37 9 84 32 45 19 341 80 40 74 22 38 .785 .38 0 N .785
16 .613 41200 53 13 36 15 73 29 44 19 404 80 39 65 16 29 .804 .23 0 N .804
17 -.186 40994 95 19 37 9 103 41 45 20 441 80 40 91 60 55 -.137 .56 0 N -.137
18 1.851 40788 177 44 37 9 611 205 45 20 412 80 40 545 145 545 1.908 .93 0 N 1.908
19 .682 40582 1158 349 37 9 2059 594 45 20 440 80 40 1838 1095 2060 .911 .98 0 N .911
20 -.231 40376 539 228 38 9 525 240 46 19 330 80 41 468 510 470 -.117 .95 0 N -.117

Total number of rows: 44290

Table truncated, full table size 3566 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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