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Status
Public on Jun 25, 2013
Title
ML-4189-TG2
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
ML-4189-TG2
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
3.703
1
21082
1246
18
8
106006
14351
37
14
1342
118
72
207854
13092
170489
3.302
.37
0
2
.579
2
30
12
18
8
46
17
37
14
1014
122
72
90
8
13
.71
-1
0
3
.022
3
31
15
18
8
42
16
37
14
980
132
71
82
8
8
-.125
.45
0
4
-.801
4
1196
217
18
8
285
67
37
14
988
120
72
558
714
410
-1.276
.32
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
6
-.517
6
46
20
18
8
45
17
35
14
1010
130
68
88
21
14
-.432
.13
0
7
.003
7
31
14
17
8
42
14
36
13
976
128
70
82
9
9
0
-1
0
8
.284
8
43
19
18
8
52
19
36
13
992
124
70
101
18
22
.37
.45
0
9
.558
9
34
12
17
8
52
22
38
14
1014
126
74
101
13
19
.755
-1
0
10
.943
10
29
13
18
9
48
19
37
14
1038
128
72
94
8
15
1.138
-1
0
11
.157
11
34
15
18
9
44
15
36
14
954
128
70
86
11
12
.193
-1
0
12
.087
12
587
80
18
9
253
50
35
14
1002
116
68
496
342
363
-.405
.38
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
14
.362
14
31
10
18
8
44
13
37
13
1004
116
72
86
8
11
.223
.31
0
15
-.336
15
47
18
18
8
50
22
38
13
1012
128
74
98
21
17
-.223
-1
0
16
.313
16
28
10
17
8
41
10
36
15
1022
110
70
80
6
8
.152
-1
0
17
-1.411
17
346
49
17
9
79
29
38
14
1002
116
74
154
191
71
-2.029
.51
0
18
.633
18
26
11
18
8
41
13
37
13
1024
116
72
80
5
8
0
-1
0
19
1.05
19
51
15
18
8
69
23
36
13
1008
120
70
135
23
48
1.022
.4
0
20
.313
20
3522
568
18
8
1703
385
36
12
1018
126
70
3339
2168
2693
-.1
.67
0
243504 17984 Kbytes .Supplementary data files not provided Processed data included within Sample table
