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Status
Public on Jun 25, 2013
Title
Baylor 4913 TG1
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, 38:121-124
Channel 2 Source name
Baylor 4913 TG1
Organism
Homo sapiens Characteristics
tumor: Xenograft
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
Xenograft
Data processing
Data for both channels were Lowess-normalized and then log(2) ratio was taken
Submission date
Dec 12, 2011
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)
GSE34412 A Renewable Tissue Resource of Phenotypically Stable, Biologically and Ethnically Diverse, Patient-derived Human Breast Cancer Xenografts
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
.785
1
47890
2567
17
8
95991
16440
37
14
1364
110
40
105484
51632
88969
1.139
.5
0
2
.938
2
21
8
18
8
41
14
37
14
1008
120
40
45
3
6
1.322
-1
0
3
-.046
3
23
10
19
9
40
14
37
14
1044
116
40
43
4
3
0
-1
0
4
-.671
4
438
110
19
8
282
96
36
14
982
122
39
309
405
254
-.635
.76
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
6
-1.071
6
27
12
18
8
39
13
36
14
1032
128
39
42
8
4
-1.415
-1
0
7
-.26
7
24
8
18
8
40
13
36
13
1004
126
39
43
6
5
-.584
.44
0
8
.155
8
33
16
17
8
52
15
36
13
1016
124
39
57
15
17
.363
-1
0
9
-1.49
9
29
13
17
8
40
15
37
13
1064
130
40
43
11
4
-1.737
.28
0
10
-.378
10
24
10
17
8
40
14
36
14
986
124
39
43
6
5
-.322
.36
0
11
.412
11
26
10
18
8
46
16
37
14
1004
118
40
50
7
10
.515
.47
0
12
-1.718
12
411
107
18
8
143
47
37
13
1016
126
40
157
371
112
-1.747
.47
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
14
.076
14
24
9
17
8
44
19
38
14
970
126
41
48
6
7
.223
-1
0
15
.085
15
32
11
18
9
52
17
39
14
1034
118
42
57
13
14
.322
.3
0
16
-.367
16
27
12
17
8
46
16
39
13
1008
126
42
50
9
7
0
.13
0
17
-.942
17
424
94
18
8
232
92
38
14
1018
128
41
254
389
202
-.924
.53
0
18
-.376
18
26
11
17
7
44
18
38
14
988
130
41
48
8
6
-.193
.32
0
19
-.052
19
31
13
18
8
47
15
36
14
1008
120
39
51
12
12
0
.27
0
20
.066
20
2218
332
18
8
2658
587
38
14
1002
102
41
2920
2346
2456
.388
.79
0
243504 17758 Kbytes .Supplementary data files not provided Processed data included within Sample table
