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Sample GSM1008915 Query DataSets for GSM1008915
Status Public on Jul 29, 2014
Title SUM1315
Sample type RNA
 
Channel 1
Source name Human Reference
Organism Homo sapiens
Characteristics reference: Whole human total RNA
Biomaterial provider Perou Lab-UNC-CH
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-150
 
Channel 2
Source name 9830-000060B NEW PROTOCOL V114
Organism Homo sapiens
Characteristics sample: Cell Line
Biomaterial provider Perou Lab-UNC-CH
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 Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.
Description Cell Line
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Sep 24, 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 GPL8269
Series (1)
GSE41119 Molecular Characterization of Basal-like and Non-Basal-like Triple-Negative Breast Cancers

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 .044 1 44987 4319 19 8 62953 14103 34 13 1358 124 61 114459 52380 54015 1.347 .36 0
2 .199 2 28 12 20 9 35 15 34 13 1010 120 61 63 3 3 -2 .04 0
3 0 3 26 10 19 9 34 13 35 13 994 120 63 61 0 0 0 -1 0
4 -.641 4 622 129 20 9 381 142 33 14 1008 124 59 692 571 366 .077 .69 0
5 0 5 1 1 1 1 1 0 0 1 2 2 0 1 0 0 0 1 0
6 .083 6 37 12 19 8 43 18 33 13 986 122 59 78 13 13 .249 .2 0
7 -.028 7 34 15 18 8 41 16 35 14 1036 116 63 74 10 10 -.347 .09 0
8 -1.254 8 43 14 19 8 37 14 33 13 1006 118 59 67 16 6 -1.523 -1 0
9 .372 9 35 15 18 8 46 15 34 14 1006 126 61 83 12 16 .553 -1 0
10 .152 10 34 15 19 8 41 18 33 13 992 130 59 74 10 11 0 -1 0
11 -.012 11 35 15 18 8 42 17 34 13 1036 120 61 76 12 12 -.092 .27 0
12 -1.848 12 586 129 19 9 170 53 34 14 990 124 61 309 527 146 -1.191 .53 0
13 0 13 1 1 1 1 1 0 0 1 2 2 0 1 0 0 0 1 0
14 .882 14 30 12 19 9 43 16 34 13 1032 130 61 78 7 13 .918 .19 0
15 .308 15 46 17 19 8 56 21 34 13 1020 112 61 101 22 27 .621 -1 0
16 .905 16 29 14 19 9 41 14 34 13 1006 128 61 74 6 12 .53 -1 0
17 -.038 17 565 117 19 9 518 185 33 13 1062 124 59 941 522 508 .694 .65 0
18 .867 18 29 13 18 8 42 14 35 14 960 128 63 76 6 12 .53 .1 0
19 -.392 19 38 15 18 8 42 17 34 13 980 118 61 76 15 11 -.342 -1 0
20 .361 20 2752 552 18 8 3851 1437 34 12 990 128 61 7001 2851 3661 1.344 .64 0

Total number of rows: 243504

Table truncated, full table size 17897 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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