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Status
Public on Jun 25, 2013
Title
Baylor 2665A TG6
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 2665A TG6
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
.497
1
61848
5921
16
7
84694
12906
38
14
1336
126
55
122744
60901
85951
.988
.44
0
2
1.007
2
25
10
16
8
48
16
38
14
1000
128
55
69
7
14
.807
-1
0
3
.44
3
23
10
16
8
40
14
37
13
1008
124
53
57
4
5
-.584
.23
0
4
-.332
4
854
162
16
7
535
186
38
14
1010
118
55
775
724
575
-.218
.81
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
6
-1.073
6
35
18
17
8
43
17
39
14
1014
124
56
62
13
6
-1.586
.54
0
7
.39
7
29
12
17
8
46
15
37
13
996
124
53
66
9
12
.241
-1
0
8
-.328
8
52
20
17
7
57
20
37
13
978
120
53
82
30
24
-.229
.18
0
9
-.753
9
45
19
17
7
50
17
39
14
960
122
56
72
23
14
-.754
.41
0
10
.069
10
30
12
17
8
46
16
39
14
1024
130
56
66
9
10
-.138
.32
0
11
.088
11
32
11
16
7
49
15
39
14
1004
120
55
71
12
13
.193
.31
0
12
-2.125
12
809
129
16
7
170
71
40
15
1006
130
57
246
671
153
-2.071
.47
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
14
.564
14
24
10
15
7
44
15
38
13
948
120
55
63
6
9
0
.4
0
15
.438
15
52
19
17
7
73
19
39
14
1030
120
56
105
30
40
.527
.47
0
16
.799
16
27
11
17
8
48
14
38
14
1028
130
55
69
8
14
.638
.29
0
17
-.165
17
1011
184
16
7
714
206
40
14
1024
116
57
1034
867
774
-.026
.65
0
18
.338
18
27
11
15
7
47
15
38
13
1034
128
55
68
9
12
.379
-1
0
19
-1.021
19
38
15
15
7
47
16
40
14
1030
124
57
68
18
9
-.932
.13
0
20
-.338
20
5637
1103
16
7
3885
1499
39
15
1004
130
56
5630
5227
4135
-.012
.78
0
243504 18013 Kbytes .Supplementary data files not provided Processed data included within Sample table
