GEO help: Mouse over screen elements for information.
Status
Public on Jun 25, 2013
Title
ML-5097-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-5097-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
5.33
1
14870
1132
19
8
66809
7293
38
14
1390
114
90
159069
4965
199715
3.42
.71
0
2
-.284
2
37
13
20
9
43
13
38
13
994
126
90
102
11
9
-.502
-1
0
3
-.072
3
36
13
19
8
46
18
39
13
1002
124
92
109
11
10
.087
.31
0
4
.146
4
767
176
18
9
146
45
38
14
1014
126
90
347
271
300
-1.54
.48
0
5
0
5
1
1
1
1
1
0
0
1
2
2
0
2
0
0
0
1
0
6
.418
6
48
17
18
9
51
18
37
13
1016
118
88
121
18
24
.238
.41
0
7
-.912
7
40
15
18
8
41
15
37
14
1020
126
88
97
14
7
-1.221
.25
0
8
.41
8
44
13
18
9
50
17
37
14
1062
122
88
119
16
21
.37
.37
0
9
-.287
9
38
15
18
9
45
17
38
14
1040
130
90
107
13
10
-.083
.26
0
10
.407
10
40
15
19
9
48
17
37
14
1022
122
88
114
13
18
.452
-1
0
11
.619
11
36
19
19
9
48
14
37
14
978
128
88
114
11
17
.7
-1
0
12
-2.813
12
526
108
19
9
51
16
38
14
976
130
90
121
218
31
-4.035
-1
0
13
0
13
1
1
1
1
1
0
0
1
2
2
0
2
0
0
0
1
0
14
.26
14
41
14
19
10
49
16
38
14
1022
132
90
116
14
17
.379
-1
0
15
-.638
15
53
19
18
9
47
18
38
15
1008
120
90
111
22
14
-.694
.09
0
16
-.068
16
38
14
18
9
46
18
38
16
1032
120
90
109
13
12
.079
-1
0
17
-.29
17
320
69
19
9
79
30
38
15
1020
130
90
188
122
100
-1.613
-1
0
18
.407
18
35
13
20
9
46
16
38
14
1032
128
89
109
10
13
.515
-1
0
19
.407
19
46
14
19
9
51
20
37
13
1002
126
88
121
17
22
.344
-1
0
20
1.543
20
2580
413
19
9
888
233
37
14
1018
122
88
2114
865
2521
-.338
.55
0
243504 17802 Kbytes .Supplementary data files not provided Processed data included within Sample table
