GEO help: Mouse over screen elements for information.
Status
Public on Jun 25, 2013
Title
Baylor 4888 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 4888 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
-.435
1
56091
4617
18
8
81094
17662
38
14
1378
108
38
81094
78381
57986
.532
.57
0
2
-.018
2
24
12
19
8
42
16
39
13
1046
126
39
42
4
4
-.415
-1
0
3
-.59
3
24
11
19
8
40
15
39
14
1010
124
39
40
3
2
-2.322
-1
0
4
-.423
4
500
110
17
8
509
184
37
14
968
118
37
509
553
413
-.031
.67
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
6
-.165
6
31
13
18
8
49
14
38
15
1012
122
38
49
13
11
-.125
-1
0
7
-.278
7
26
11
17
8
42
15
37
13
996
122
37
42
7
6
-.486
.05
0
8
-.678
8
38
14
18
8
51
19
38
13
1028
116
38
51
20
13
-.548
-1
0
9
-.408
9
36
16
19
8
51
17
38
14
1010
118
38
51
17
13
-.3
.35
0
10
-.403
10
28
9
18
8
45
16
39
15
1014
118
39
45
9
7
-.584
.1
0
11
.036
11
30
14
18
8
50
18
38
14
1010
126
38
50
11
12
.263
-1
0
12
-1.368
12
489
110
18
8
269
93
38
14
1016
122
38
269
531
205
-1.026
.57
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
1
0
0
0
1
0
14
.984
14
25
11
19
8
48
18
37
13
1028
112
37
48
6
12
.874
-1
0
15
-.958
15
37
16
19
8
47
14
38
15
1016
120
38
47
18
9
-1
-1
0
16
.711
16
26
13
19
8
49
19
39
15
1026
116
39
49
6
11
.737
-1
0
17
-.566
17
427
103
18
8
393
155
38
14
1020
122
38
393
464
313
-.201
.47
0
18
.553
18
26
12
19
9
45
17
37
15
1082
124
37
45
6
9
.415
-1
0
19
.971
19
30
12
19
8
59
24
36
15
1030
124
36
59
11
23
1.202
.18
0
20
.767
20
2597
501
18
9
7171
2905
37
14
1016
122
36
7171
3288
5596
1.469
.67
0
243504 17895 Kbytes .Supplementary data files not provided Processed data included within Sample table
