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Status
Public on Jun 25, 2013
Title
Baylor 4664 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 4664 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
.446
1
52897
4668
17
7
84258
10623
39
14
1394
116
37
81803
57171
77896
.629
.47
0
2
-.586
2
23
11
18
8
42
15
39
13
1020
122
37
40
5
3
-.415
.33
0
3
.558
3
21
8
18
8
41
15
37
13
1022
124
35
39
3
4
2
-1
0
4
.77
4
461
106
18
8
777
337
37
12
1034
128
35
754
438
747
.705
.44
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
0
0
0
0
1
0
6
.754
6
29
11
18
8
57
19
38
14
1026
112
36
55
11
19
1.078
-1
0
7
-.669
7
25
11
18
7
40
16
36
14
974
124
34
38
7
4
-.584
.32
0
8
.262
8
33
13
18
7
55
20
37
13
1004
126
35
53
15
18
.363
.19
0
9
-.523
9
29
12
19
8
45
17
37
14
1028
118
35
43
11
8
-.322
.3
0
10
-.059
10
26
11
18
8
46
16
38
14
974
126
36
44
8
8
.193
.29
0
11
1.724
11
20
9
18
8
46
17
37
14
1006
122
35
44
2
9
3.17
-1
0
12
-2.242
12
434
80
18
8
116
52
37
14
994
132
35
112
396
83
-2.427
.34
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
0
0
0
0
1
0
14
-.145
14
23
10
19
8
40
14
37
14
1012
122
35
38
4
3
0
-1
0
15
1.097
15
31
12
19
8
63
26
37
14
996
124
35
61
12
26
1.241
.48
0
16
-.706
16
24
10
18
8
42
13
38
14
1078
120
36
40
6
4
-.322
.22
0
17
-.475
17
401
76
18
8
294
113
36
13
1050
120
34
285
371
267
-.606
.43
0
18
-.478
18
24
10
18
8
40
13
36
14
1028
134
34
38
6
4
-.322
.4
0
19
.196
19
28
13
18
8
49
16
37
13
1012
124
35
47
10
12
.585
-1
0
20
1.068
20
2400
282
18
8
5424
1860
37
13
1006
108
35
5266
2473
5187
1.136
.73
0
243504 17800 Kbytes .Supplementary data files not provided Processed data included within Sample table
