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Sample GSM912194 Query DataSets for GSM912194
Status Public on Jan 01, 2014
Title T47D_3D_202-22
Sample type RNA
 
Channel 1
Source name Stratagene Human Universal Reference
Organism Homo sapiens
Characteristics reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Biomaterial provider Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name T47D_3D_202-22
Organism Homo sapiens
Characteristics sample: T47D_3D_202-22
cell type: established breast cancer cells
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
Description RNA from a primary culture cell line
established breast cancer cells
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Apr 10, 2012
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 GPL10481
Series (1)
GSE37145 Vascular properties of breast cancer intrinsic subtypes

Data table header descriptions
ID_REF Spot Reference ID
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
SPOT spot number on array
CH1_MEAN
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 channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots

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
1 .105 1 2589 388 23 11 2432 690 37 13 1346 110 108 7152 2391 2571 1.457 -1 0
2 -.828 2 44 17 24 11 38 10 37 14 1010 116 108 111 7 4 -2.662 .45 0
3 .944 3 37 12 26 11 42 13 38 14 1038 118 111 123 5 10 .263 -1 0
4 .133 4 40 16 24 11 41 14 37 13 1030 122 108 120 8 9 -.223 -1 0
5 1.133 5 36 15 24 10 44 14 37 13 1054 128 108 129 6 13 1.07 -1 0
6 .424 6 39 15 23 9 44 16 37 13 1008 132 108 129 9 12 .485 -1 0
7 -.717 7 46 17 25 10 41 12 39 13 1020 128 113 120 9 5 -1.515 -1 0
8 .136 8 42 18 24 10 43 15 37 14 1048 124 108 126 10 11 .083 -1 0
9 .043 9 42 15 25 10 41 13 37 14 996 126 108 120 9 9 -.415 .17 0
10 -.169 10 42 18 24 10 42 14 38 14 1016 126 110 123 9 8 -.386 -1 0
11 .819 11 39 11 25 10 46 16 38 14 1000 118 111 135 8 14 .884 .41 0
12 -.371 12 47 17 26 11 46 16 42 15 1058 124 123 135 11 8 -.662 -1 0
13 -.071 13 112 37 24 11 87 23 41 14 1038 118 120 255 65 62 .667 -1 0
14 .275 14 76 23 25 11 66 27 37 13 1058 118 108 194 35 43 .782 .39 0
15 1.086 15 49 16 25 10 60 20 38 14 1024 124 111 176 16 35 1.437 .1 0
16 -.146 16 60 21 24 10 52 15 39 13 996 120 113 152 23 21 .198 -1 0
17 -1.384 17 47 17 24 11 39 13 38 14 1066 120 111 114 7 3 -2.878 .38 0
18 .295 18 103 39 24 11 93 32 39 14 1064 126 114 273 59 72 1.027 .47 0
19 .374 19 43 19 24 11 47 15 38 14 1056 124 111 138 11 15 .585 .39 0
20 .506 20 702 252 25 11 786 321 39 13 1060 120 114 2311 597 848 1.698 .85 0

Total number of rows: 45220

Table truncated, full table size 3335 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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