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Status
Public on Jul 09, 2008
Title
Upper respiratory tract infection (Viro3P10-010)
Sample type
RNA
Source name
RdABC amplified RNA from Nasal Lavage
Organism
Viruses Characteristics
Upper respiratory tract infection
Extracted molecule
total RNA
Extraction protocol
RNeasy followed by DNAse treatment
Label
Cy3
Label protocol
Rd C Cy3 incorporation
Hybridization protocol
standard overnight hybridization
Scan protocol
Axon 4000 scanner
Description
RdABC amplified RNA from Nasal Lavage
Data processing
Median feature intensity minus median background intensity. The data analysis software used is E-Predict, which normalizes the data using a variety of measures: sum, quadratic, unit-vector, or no normalization (please see Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30). E-Predict is public access. For the purposes of this paper, sum-normalized intensities were used in the analysis.
Submission date
Jan 28, 2008
Last update date
Jul 09, 2008
Contact name
Joe DeRisi
E-mail(s)
joe@derisilab.ucsf.edu Phone
415-476-4132
URL
http://derisilab.ucsf.edu Organization name
University of California, San Francisco
Department
Biochemistry and Biophysics
Lab
Joseph DeRisi Laboratory
Street address
City
San Francisco
State/province
CA
ZIP/Postal code
94107
Country
USA
Platform ID
GPL3429 Series (1)
Data table header descriptions ID_REF VALUE same as UNF_VALUE but with flagged values removed
CH1_MEDIAN Channel 1 intensity median
CH1_MEAN Channel 1 intensity mean
CH1_SD Channel 1 intensity standard deviation
CH1_BGD_MEDIAN Channel 1 background intensity median
CH1_BGD_MEAN Channel 1 background intensity mean
CH1_BGD_SD Channel 1 background intensity standard deviation
CH1_NET_MEDIAN Channel 1 net intensity median
CH1_NET_MEAN Channel 1 net intensity median
FLAG GenePix spot flag
UNF_VALUE Channel 1 net intensity median (same as CH1_NET_MEDIAN)
Data table ID_REF VALUE CH1_MEDIAN CH1_MEAN CH1_SD CH1_BGD_MEDIAN CH1_BGD_MEAN CH1_BGD_SD CH1_NET_MEDIAN CH1_NET_MEAN FLAG UNF_VALUE 1
46
105
105
27
59
61
17
46
46
46
2
48
106
105
29
58
60
16
48
47
48
3
88
148
149
30
60
62
18
88
89
88
4
43
100
102
23
57
59
15
43
45
43
5
56
112
110
32
56
58
15
56
54
56
6
51
114
118
21
63
64
16
51
55
51
7
47
105
109
24
58
59
15
47
51
47
8
71
128
132
24
57
58
14
71
75
71
9
39
99
98
27
60
61
17
39
38
39
10
60
119
121
31
59
60
15
60
62
60
11
98
160
163
47
62
63
16
98
101
98
12
123
187
195
52
64
64
18
123
131
123
13
54
112
113
25
58
59
15
54
55
54
14
67
124
118
29
57
59
15
67
61
67
15
183
245
239
72
62
64
16
183
177
183
16
200
259
242
88
59
61
15
200
183
200
17
42
124
121
24
82
82
16
42
39
42
18
60
136
130
38
76
77
20
60
54
60
19
79
157
155
36
78
80
20
79
77
79
20
89
172
171
32
83
85
23
89
88
89
21888 828 Kbytes .Supplementary file Size Download File type/resource GSM259928.gpr.gz
1.7 Mb
(ftp) (http) GPR
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